diff --git a/README.md b/README.md index 0b095dc..f31c1f7 100644 --- a/README.md +++ b/README.md @@ -7,9 +7,12 @@ All versions -- current and prior -- are available via Zenodo DOIs, with the lat ## The paper -The paper was just submitted (Sept. 10, 2016) to [bioRxiv](http://biorxiv.org/content/early/2016/09/11/074625) and Annual Reviews in Biophysics. Its source files are deposited here, as detailed below, and comments/suggestions, etc. are welcome via the issue tracker (https://github.com/MobleyLab/benchmarksets/issues). +Versions of this paper are archived on [bioRxiv](http://biorxiv.org/content/early/2016/09/11/074625); additionally, an early version is being published in Annual Reviews in Biophysics. Source files for the paper are deposited here, as detailed below, and comments/suggestions, etc. are welcome via the issue tracker (https://github.com/MobleyLab/benchmarksets/issues). + +This work is posted with permission from the Annual Review of Biophysics, Volume 46 © 2017 by [Annual Reviews](http://www.annualreviews.org/). Only the Annual Reviews version fo the work is peer reviewed; versions posted here are effectively preprints updated at the authors' discretion. The right to create derivative works (exercised here) is also exercised with permission from the Annual Review of Biophysics, Volume 46 © 2017 by Annual Reviews, http://www.annualreviews.org/ + +A list of authors is provided below. -The paper's authors are David L. Mobley (UC Irvine) and Michael K. Gilson (UCSD). ## The vision @@ -56,19 +59,32 @@ If you have a specific suggestion or request relating to the material on GitHub ### Submit a pull request -We also welcome contributions to the material which is already here to extend it (see Section IV in our paper) and encourage you to actually propose changes via a "pull request", even to the paper itself. This will allow us to track your contributions, as well. Specifically, the full list of contributors to the updated paper and data can be appended to subsequent versions of this work, as they would be for a software project. +We also welcome contributions to the material which is already here to extend it (see Section IV in our paper) and encourage you to actually propose changes via a "pull request", even to the paper itself. This will allow us to track your contributions, as well. Specifically, the full list of contributors to the updated paper and data can be appended to subsequent versions of this work, as they would be for a software project. New versions of this work are assigned unique, cite-able DOIs and essentially constitute preprints, so they can be cited as interim research products. + +## Authors +- David L. Mobley (UCI) +- Michael K. Gilson (UCSD) + +Your name, too, can go here if you help us substantially revise/extend the paper. + + +## Acknowledgments + +We want to thank the following people who contributed to this repository and the paper, in addition to those acknowledged within the [text itself](https://github.com/MobleyLab/benchmarksets/blob/master/paper/benchmarkset.pdf) -## Contributors - David Slochower (UCSD, Gilson lab): Grammar corrections and improved table formatting - Nascimento (in a comment on biorxiv): Highlighted PDB code error for n-phenylglycinonitrile - Jian Yin (UCSD, Gilson lab): Provided host-guest structures and input files for the host-guest sets described in the paper +Please note that GitHub's automatic "contributors" list does not provide a full accounting of everyone contributing to this work, as some contributions have been received by e-mail or other mechanisms. + ## Versions - [v1.0](https://github.com/MobleyLab/benchmarksets/releases/tag/v1.0): As posted to bioRxiv - v1.0.1 ([10.5281/zenodo.155330](https://doi.org/10.5281/zenodo.15533)): Incorporating improved tables and typo fixes from D. Slochower; also, versions now have unique DOIs via Zenodo. - v1.0.4 ([10.5281/zenodo.167349](http://doi.org/10.5281/zenodo.167349)): Maintenance version fixing an incorrect PDB code and adding a new reference and some new links. - v1.1 ([10.5281/zenodo.197428](http://doi.org/10.5281/zenodo.197428)): Adds significant additional discussion on potential future benchmark sets, needs for workflow science, etc. See release notes for more details. Versions also now include the date and version number within the PDF. - v1.1.1 ([10.5281/zenodo.254619](http://doi.org/10.5281/zenodo.254619)): Adds input files for host-guest benchmarks; some revisions to text as recommended by Annual Reviews. See release notes for more details. +- v1.1.2: Adds consistently handled SMILES for aromatics, Annual Reviews copyright/rights info in TeX and README, additional citation information for one reference, and new discussion of some new bromodomain absolute binding free energy work. ## Changes not yet in a release diff --git a/paper/benchmarkset.bib b/paper/benchmarkset.bib index 3383e2e..a9b816a 100644 --- a/paper/benchmarkset.bib +++ b/paper/benchmarkset.bib @@ -24,11 +24,12 @@ @article{henriksen_computational_2015 year = {2015}, keywords = {alchemical,CB7,cucurbituril,host–guest complexation}, pages = {4377--4394}, - file = {b00405.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/83KZV5MM/b00405.pdf:application/pdf} + file = {b00405.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/83KZV5MM/b00405.pdf:application/pdf}, + groups = {CB7,cyclodextrin,MKG} } @article{monroe_converging_2014, - title = {Converging Free Energies of Binding in cucurbit[7]uril and Octa-Acid Host\textendash{}guest Systems from {{SAMPL4}} Using Expanded Ensemble Simulations}, + title = {Converging Free Energies of Binding in Cucurbit[7]Uril and Octa-Acid Host\textendash{}guest Systems from {{SAMPL4}} Using Expanded Ensemble Simulations}, volume = {28}, issn = {0920-654X, 1573-4951}, doi = {10.1007/s10822-014-9716-4}, @@ -43,7 +44,8 @@ @article{monroe_converging_2014 year = {2014}, keywords = {alchemical,CB7,host–guest complexation,OctaAcid,SAMPL,SAMPL4}, pages = {401--415}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NRVQCRED/Monroe and Shirts - 2014 - Converging free energies of binding in cucurbit[7].pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q76K952R/s10822-014-9716-4.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NRVQCRED/Monroe and Shirts - 2014 - Converging free energies of binding in cucurbit[7].pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q76K952R/s10822-014-9716-4.html:text/html}, + groups = {CB7,OctaAcid} } @article{fenley_bridging_2014, @@ -61,7 +63,8 @@ @article{fenley_bridging_2014 year = {2014}, keywords = {alchemical,CB7,host–guest complexation}, pages = {4069--4078}, - file = {ct5004109.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/XBMTZJTU/ct5004109.pdf:application/pdf} + file = {ct5004109.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/XBMTZJTU/ct5004109.pdf:application/pdf}, + groups = {CB7} } @article{wickstrom_parameterization_2016, @@ -81,7 +84,8 @@ @article{wickstrom_parameterization_2016 year = {2016}, keywords = {alchemical,BEDAM,beta cyclodextrin,force field,Free energy,GIST,host–guest complexation,OPLS}, pages = {10--21}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZBJKTE93/Wickstrom et al. - 2016 - Parameterization of an effective potential for pro.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NSI4KNUQ/full.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZBJKTE93/Wickstrom et al. - 2016 - Parameterization of an effective potential for pro.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NSI4KNUQ/full.html:text/html}, + groups = {cyclodextrin} } @article{yin_toward_2015, @@ -99,11 +103,12 @@ @article{yin_toward_2015 year = {2015}, keywords = {alchemical,CB7,host–guest complexation}, pages = {10145--10155}, - file = {acs%2Ejpcb%2E5b04262.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UXST6U4T/acs%2Ejpcb%2E5b04262.pdf:application/pdf} + file = {acs%2Ejpcb%2E5b04262.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UXST6U4T/acs%2Ejpcb%2E5b04262.pdf:application/pdf}, + groups = {CB7} } @article{muddana_blind_2014, - title = {Blind Prediction of {{SAMPL4}} cucurbit[7]uril Binding Affinities with the Mining Minima Method}, + title = {Blind Prediction of {{SAMPL4}} Cucurbit[7]Uril Binding Affinities with the Mining Minima Method}, volume = {28}, issn = {0920-654X, 1573-4951}, doi = {10.1007/s10822-014-9726-2}, @@ -118,7 +123,8 @@ @article{muddana_blind_2014 year = {2014}, keywords = {alchemical,CB7,cucurbituril,host–guest complexation,SAMPL,SAMPL4}, pages = {463--474}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/P4GC5C8T/Muddana et al. - 2014 - Blind prediction of SAMPL4 cucurbit[7]uril binding.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FUMU345G/s10822-014-9726-2.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/P4GC5C8T/Muddana et al. - 2014 - Blind prediction of SAMPL4 cucurbit[7]uril binding.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FUMU345G/s10822-014-9726-2.html:text/html}, + groups = {CB7} } @article{brown_healthy_2009, @@ -155,7 +161,8 @@ @article{gibb_well-defined_2004 year = {2004}, keywords = {experiment,host–guest complexation,OctaAcid}, pages = {11408--11409}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/KZH98I6W/Gibb and Gibb - 2004 - Well-Defined, Organic Nanoenvironments in Water .pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZF42DDDQ/ja0475611.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/KZH98I6W/Gibb and Gibb - 2004 - Well-Defined, Organic Nanoenvironments in Water .pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZF42DDDQ/ja0475611.html:text/html}, + groups = {OctaAcid} } @article{sokkalingam_binding_2016, @@ -173,7 +180,8 @@ @article{sokkalingam_binding_2016 year = {2016}, keywords = {binding free energy,experiment,host–guest complexation,ion binding,OA}, pages = {48--51}, - file = {Gibb Text.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/58UUWX9K/Gibb Text.pdf:application/pdf} + file = {Gibb Text.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/58UUWX9K/Gibb Text.pdf:application/pdf}, + groups = {OctaAcid} } @article{carnegie_anion_2014, @@ -192,14 +200,15 @@ @article{carnegie_anion_2014 year = {2014}, keywords = {Anion,experiment,Hofmeister Effect,host–guest complexation,Hydrophobic effect,OA}, pages = {11682--11684}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AD6ZW4TV/Carnegie et al. - 2014 - Anion Complexation and The Hofmeister Effect.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/C83PMKB4/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AD6ZW4TV/Carnegie et al. - 2014 - Anion Complexation and The Hofmeister Effect.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/C83PMKB4/abstract.html:text/html}, + groups = {OctaAcid} } @article{moghaddam_new_2011, - title = {New {{Ultrahigh Affinity Host}}-{{Guest Complexes}} of {{Cucurbit}}[7]uril with {{Bicyclo}}[2.2.2]octane and {{Adamantane Guests}}: {{Thermodynamic Analysis}} and {{Evaluation}} of {{M2 Affinity Calculations}}}, + title = {New {{Ultrahigh Affinity Host}}-{{Guest Complexes}} of {{Cucurbit}}[7]Uril with {{Bicyclo}}[2.2.2]Octane and {{Adamantane Guests}}: {{Thermodynamic Analysis}} and {{Evaluation}} of {{M2 Affinity Calculations}}}, volume = {133}, issn = {0002-7863, 1520-5126}, - shorttitle = {New {{Ultrahigh Affinity Host}}-{{Guest Complexes}} of {{Cucurbit}}[7]uril with {{Bicyclo}}[2.2.2]octane and {{Adamantane Guests}}}, + shorttitle = {New {{Ultrahigh Affinity Host}}-{{Guest Complexes}} of {{Cucurbit}}[7]Uril with {{Bicyclo}}[2.2.2]Octane and {{Adamantane Guests}}}, doi = {10.1021/ja109904u}, language = {en}, timestamp = {2016-07-26T16:42:56Z}, @@ -211,7 +220,8 @@ @article{moghaddam_new_2011 year = {2011}, keywords = {CB7,experiment,host–guest complexation}, pages = {3570--3581}, - file = {ja109904u.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7CCWHP9I/ja109904u.pdf:application/pdf} + file = {ja109904u.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7CCWHP9I/ja109904u.pdf:application/pdf}, + groups = {CB7} } @article{gilson_stress_2010, @@ -230,7 +240,8 @@ @article{gilson_stress_2010 year = {2010}, keywords = {CB7,host–guest complexation}, pages = {637--646}, - file = {ct900668k.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/J75PSWNR/ct900668k.pdf:application/pdf} + file = {ct900668k.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/J75PSWNR/ct900668k.pdf:application/pdf}, + groups = {CB7} } @article{moghaddam_hostguest_2009, @@ -249,11 +260,12 @@ @article{moghaddam_hostguest_2009 year = {2009}, keywords = {CB7,host–guest complexation}, pages = {4012--4021}, - file = {ja808175m.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FCDUFSFB/ja808175m.pdf:application/pdf} + file = {ja808175m.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FCDUFSFB/ja808175m.pdf:application/pdf}, + groups = {CB7} } @article{wyman_cucurbituril_2008, - title = {Cucurbit[7]uril Host\textendash{}guest Complexes with Small Polar Organic Guests in Aqueous Solution}, + title = {Cucurbit[7]Uril Host\textendash{}guest Complexes with Small Polar Organic Guests in Aqueous Solution}, volume = {6}, issn = {1477-0520, 1477-0539}, doi = {10.1039/b801650j}, @@ -266,7 +278,8 @@ @article{wyman_cucurbituril_2008 year = {2008}, keywords = {CB7,experiment,host–guest complexation}, pages = {1796}, - file = {B801650J.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/TVXGTFP8/B801650J.pdf:application/pdf} + file = {B801650J.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/TVXGTFP8/B801650J.pdf:application/pdf}, + groups = {CB7} } @article{simonson_concepts_2016, @@ -302,13 +315,14 @@ @article{gao_binding_2015 year = {2015}, keywords = {binding enthalpy,CB7,host–guest complexation}, pages = {4555--4564}, - file = {acs%2Ejctc%2E5b00676.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/F4NVWD9F/acs%2Ejctc%2E5b00676.pdf:application/pdf} + file = {acs%2Ejctc%2E5b00676.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/F4NVWD9F/acs%2Ejctc%2E5b00676.pdf:application/pdf}, + groups = {CB7} } @article{Isaacs:2009:Chem.Commun., - title = {Cucurbit[n]urils: From Mechanism to Structure and Function}, + title = {Cucurbit[n]Urils: From Mechanism to Structure and Function}, issn = {1359-7345, 1364-548X}, - shorttitle = {Cucurbit[n]urils}, + shorttitle = {Cucurbit[n]Urils}, doi = {10.1039/B814897J}, language = {en}, timestamp = {2016-07-30T18:30:37Z}, @@ -319,11 +333,12 @@ @article{Isaacs:2009:Chem.Commun. year = {2009}, keywords = {CB7,cucurbituril,experiment}, pages = {619--629}, - file = {B814897J.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/T53RQEVA/B814897J.pdf:application/pdf} + file = {B814897J.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/T53RQEVA/B814897J.pdf:application/pdf}, + groups = {CB7} } @article{nguyen_grid_2012, - title = {Grid Inhomogeneous Solvation Theory: {{Hydration}} Structure and Thermodynamics of the Miniature Receptor cucurbit[7]uril}, + title = {Grid Inhomogeneous Solvation Theory: {{Hydration}} Structure and Thermodynamics of the Miniature Receptor Cucurbit[7]Uril}, volume = {137}, issn = {0021-9606, 1089-7690}, shorttitle = {Grid Inhomogeneous Solvation Theory}, @@ -338,11 +353,12 @@ @article{nguyen_grid_2012 year = {2012}, keywords = {CB7,cucurbituril,Entropy,Free energy,GIST,Hydrogen bonding,Solvents,Water energy interactions}, pages = {044101}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5KRZW8R6/Nguyen et al. - 2012 - Grid inhomogeneous solvation theory Hydration str.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5875GUC8/1.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5KRZW8R6/Nguyen et al. - 2012 - Grid inhomogeneous solvation theory Hydration str.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5875GUC8/1.html:text/html}, + groups = {CB7} } @article{cao_absolute_2014, - title = {Absolute and Relative Binding Affinity of cucurbit[7]uril towards a Series of Cationic Guests}, + title = {Absolute and Relative Binding Affinity of Cucurbit[7]Uril towards a Series of Cationic Guests}, volume = {26}, issn = {1061-0278}, doi = {10.1080/10610278.2013.852674}, @@ -356,7 +372,8 @@ @article{cao_absolute_2014 year = {2014}, keywords = {CB7,cucurbituril,experiment,host–guest complexation,SAMPL,SAMPL4}, pages = {251--258}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AMSNNXHI/Cao and Isaacs - 2014 - Absolute and relative binding affinity of cucurbit.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2NNAUM4M/10610278.2013.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AMSNNXHI/Cao and Isaacs - 2014 - Absolute and relative binding affinity of cucurbit.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2NNAUM4M/10610278.2013.html:text/html}, + groups = {CB7} } @article{muddana_prediction_2012, @@ -376,7 +393,8 @@ @article{muddana_prediction_2012 year = {2012}, keywords = {CB7,Free energy,host–guest complexation,SAMPL,SAMPL3}, pages = {517--525}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZJD6SRS8/Muddana and Gilson - 2012 - Prediction of SAMPL3 host–guest binding affinities.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/H83HPWZG/fulltext.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZJD6SRS8/Muddana and Gilson - 2012 - Prediction of SAMPL3 host–guest binding affinities.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/H83HPWZG/fulltext.html:text/html}, + groups = {CB7} } @misc{schreiner_theoretical_2016, @@ -387,7 +405,8 @@ @misc{schreiner_theoretical_2016 author = {Schreiner, Peter}, year = {2016}, keywords = {CB7,experiment,prediction}, - file = {Theoretical prediction of affinities to cucurbiturils – the blind prediction HYDROPHOBE Challenge — SPP 1807 Home:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/J8V3NP23/HydrophobeChallenge.html:text/html} + file = {Theoretical prediction of affinities to cucurbiturils – the blind prediction HYDROPHOBE Challenge — SPP 1807 Home:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/J8V3NP23/HydrophobeChallenge.html:text/html}, + groups = {CB7} } @article{ewell_water_2008, @@ -405,7 +424,8 @@ @article{ewell_water_2008 year = {2008}, keywords = {dewetting,host–guest complexation,OctaAcid,water}, pages = {10272--10279}, - file = {jp804429n.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/S54WNCP2/jp804429n.pdf:application/pdf} + file = {jp804429n.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/S54WNCP2/jp804429n.pdf:application/pdf}, + groups = {OctaAcid} } @article{wanjari_simulation_2013, @@ -423,7 +443,8 @@ @article{wanjari_simulation_2013 year = {2013}, keywords = {Acids,Free energy,host–guest complexation,Hydrophobic interactions,Methane,OctaAcid,Solvents}, pages = {234502}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MGD72JBG/Wanjari et al. - 2013 - Simulation optimization of spherical non-polar gue.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2XCMEGWQ/1.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MGD72JBG/Wanjari et al. - 2013 - Simulation optimization of spherical non-polar gue.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2XCMEGWQ/1.html:text/html}, + groups = {OctaAcid} } @article{gallicchio_bedam_2015-1, @@ -442,7 +463,8 @@ @article{gallicchio_bedam_2015-1 year = {2015}, keywords = {BEDAM,binding free energy,host–guest complexation,implicit solvent,OctaAcid,SAMPL,SAMPL4}, pages = {315--325}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/43VF6CMD/Gallicchio et al. - 2015 - BEDAM binding free energy predictions for the SAMP.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/PBD7BWDV/s10822-014-9795-2.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/43VF6CMD/Gallicchio et al. - 2015 - BEDAM binding free energy predictions for the SAMP.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/PBD7BWDV/s10822-014-9795-2.html:text/html}, + groups = {OctaAcid} } @article{gibb_anion_2011, @@ -460,7 +482,8 @@ @article{gibb_anion_2011 year = {2011}, keywords = {experiment,host–guest complexation,OctaAcid}, pages = {7344--7347}, - file = {ja202308n.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CK94DKUN/ja202308n.pdf:application/pdf} + file = {ja202308n.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CK94DKUN/ja202308n.pdf:application/pdf}, + groups = {OctaAcid} } @article{sun_calorimetric_2008, @@ -479,7 +502,8 @@ @article{sun_calorimetric_2008 year = {2008}, keywords = {host–guest complexation,OctaAcid}, pages = {141--147}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZSPMRX6V/Sun et al. - 2008 - Calorimetric Analysis of the 11 Complexes Formed .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NQ7VZ8C7/10610270701744302.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZSPMRX6V/Sun et al. - 2008 - Calorimetric Analysis of the 11 Complexes Formed .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NQ7VZ8C7/10610270701744302.html:text/html}, + groups = {OctaAcid} } @article{mikulskis_free-energy_2014, @@ -498,7 +522,8 @@ @article{mikulskis_free-energy_2014 year = {2014}, keywords = {alchemical,host–guest complexation,OctaAcid,SAMPL,SAMPL4}, pages = {375--400}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/26ITGVPJ/Mikulskis et al. - 2014 - Free-energy perturbation and quantum mechanical st.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ET79ZEFJ/10.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/26ITGVPJ/Mikulskis et al. - 2014 - Free-energy perturbation and quantum mechanical st.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ET79ZEFJ/10.html:text/html}, + groups = {OctaAcid} } @article{gibb_guests_2009, @@ -517,7 +542,8 @@ @article{gibb_guests_2009 year = {2009}, keywords = {experiment,host–guest complexation,OctaAcid}, pages = {7240--7248}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/4FMWUMN7/Gibb and Gibb - 2009 - Guests of differing polarities provide insight int.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7XEX4GWD/S0040402009001744.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/4FMWUMN7/Gibb and Gibb - 2009 - Guests of differing polarities provide insight int.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7XEX4GWD/S0040402009001744.html:text/html}, + groups = {OctaAcid} } @article{Xi:1998:Chem.Commun., @@ -536,7 +562,8 @@ @article{Xi:1998:Chem.Commun. year = {1998}, keywords = {experiment,host–guest complexation,OctaAcid}, pages = {1743--1744}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HJEA5MM6/Xi and Gibb - 1998 - Deep-cavity cavitands synthesis and solid state s.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WJGJPGM2/a803571g.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HJEA5MM6/Xi and Gibb - 1998 - Deep-cavity cavitands synthesis and solid state s.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WJGJPGM2/a803571g.html:text/html}, + groups = {OctaAcid} } @article{lin_overview_2014, @@ -572,7 +599,8 @@ @article{gan_nonmonotonic_2011 year = {2011}, keywords = {experiment,host–guest complexation,OAMe,OctaAcid,TEMOA}, pages = {4770--4773}, - file = {ja200633d.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/TM274JIG/ja200633d.pdf:application/pdf} + file = {ja200633d.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/TM274JIG/ja200633d.pdf:application/pdf}, + groups = {OctaAcid} } @article{gibb_binding_2013, @@ -591,7 +619,8 @@ @article{gibb_binding_2013 year = {2013}, keywords = {experiment,host–guest complexation,OctaAcid,SAMPL,SAMPL4}, pages = {319--325}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/37DJAJ5Q/Gibb and Gibb - 2013 - Binding of cyclic carboxylates to octa-acid deep-c.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/IK59HCQR/10.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/37DJAJ5Q/Gibb and Gibb - 2013 - Binding of cyclic carboxylates to octa-acid deep-c.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/IK59HCQR/10.html:text/html}, + groups = {OctaAcid} } @article{hsiao_prediction_2014, @@ -610,7 +639,8 @@ @article{hsiao_prediction_2014 year = {2014}, keywords = {binding free energy,CB7,host–guest complexation,metadynamics,SAMPL,SAMPL4}, pages = {443--454}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SIHP3AD8/Hsiao and Söderhjelm - 2014 - Prediction of SAMPL4 host–guest binding affinities.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/J7DCAE3Z/10.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SIHP3AD8/Hsiao and Söderhjelm - 2014 - Prediction of SAMPL4 host–guest binding affinities.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/J7DCAE3Z/10.html:text/html}, + groups = {CB7} } @article{bhakat_resolving_2016, @@ -620,7 +650,8 @@ @article{bhakat_resolving_2016 author = {Bhakat, Soumendranath and S{\"o}derhjelm, P{\"a}r}, year = {2016}, keywords = {binding free energy,host–guest complexation,metadynamics,OctaAcid,SAMPL,SAMPL5}, - file = {JCAM-D-16-00194.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5PBMP7HI/JCAM-D-16-00194.pdf:application/pdf} + file = {JCAM-D-16-00194.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5PBMP7HI/JCAM-D-16-00194.pdf:application/pdf}, + groups = {OctaAcid} } @article{pal_combined_2016, @@ -630,17 +661,22 @@ @article{pal_combined_2016 author = {Pal, Rajat Kumar and Haider, Kamran and Kaur, Divya and Flynn, William and Xia, Junchao and Levy, Ronald M. and Taran, Tetiana and Wickstrom, Lauren and Kurtzman, Tom and Gallicchio, Emilio}, year = {2016}, keywords = {alchemical,BEDAM,binding free energy,host–guest complexation,OctaAcid,SAMPL,SAMPL5}, - file = {JCAM-D-16-00173 (1).pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7V2PUB89/JCAM-D-16-00173 (1).pdf:application/pdf} + file = {JCAM-D-16-00173 (1).pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7V2PUB89/JCAM-D-16-00173 (1).pdf:application/pdf}, + groups = {OctaAcid} } @article{yin_sampl5_2016, - title = {The {{SAMPL5 Host}}-{{Guest Challenge}}: {{Binding Free Energies}} and {{Enthalpies}} from {{Explicit Solvent Simulations}}}, - timestamp = {2016-08-12T21:39:14Z}, + title = {The {{SAMPL5 Host}}-{{Guest Challenge}}: {{Computing Binding Free Energies}} and {{Enthalpies}} from {{Explicit Solvent Simulations}} by the {{Attach}}-{{Pull}}-{{Release}} ({{APR}}) {{Method}}}, + doi = {10.1007/s10822-016-9970-8}, + timestamp = {2017-03-01T18:17:17Z}, + number = {31}, journal = {J Comput Aided Mol Des}, author = {Yin, Jian and Henriksen, Niel M. and Slochower, David R. and Gilson, Michael K.}, - year = {2016}, + year = {2017}, keywords = {alchemical,binding free energy,host–guest complexation,SAMPL,SAMPL5}, - file = {JCAM-D-16-00203 (1).pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AZI7FQNU/JCAM-D-16-00203 (1).pdf:application/pdf} + pages = {133--145}, + file = {10.1007s10822-014-9718-2.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/XFTV499F/10.1007s10822-014-9718-2.pdf:application/pdf}, + groups = {OctaAcid} } @article{bosisio_blinded_2016, @@ -650,7 +686,8 @@ @article{bosisio_blinded_2016 author = {Bosisio, Stefano and Mey, Antonia S. J. S. and Michel, Julien}, year = {2016}, keywords = {alchemical,binding free energy,CBClip,host–guest complexation,OctaAcid,SAMPL,SAMPL5,standard binding free energy,standard state}, - file = {JCAM-D-16-00176_R1 (1).pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/VP99HX8Q/JCAM-D-16-00176_R1 (1).pdf:application/pdf} + file = {JCAM-D-16-00176_R1 (1).pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/VP99HX8Q/JCAM-D-16-00176_R1 (1).pdf:application/pdf}, + groups = {OctaAcid} } @article{aldeghi_accurate_2016, @@ -667,7 +704,8 @@ @article{aldeghi_accurate_2016 year = {2016}, keywords = {absolute binding free energy,alchemical,bromodomains,force field accuracy,prospective}, pages = {207--218}, - file = {C5SC02678D.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HP6P59FA/C5SC02678D.pdf:application/pdf} + file = {C5SC02678D.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HP6P59FA/C5SC02678D.pdf:application/pdf}, + groups = {bromodomains} } @article{tofoleanu_absolute_2016, @@ -677,7 +715,8 @@ @article{tofoleanu_absolute_2016 author = {Tofoleanu, Florentina and Lee, Juyong and Pickard IV., Frank C. and K{\"o}nig, Gerhard and Huang, Jing and Baek, Minkyung and Seok, Chaok and Brooks, Bernard R.}, year = {2016}, keywords = {absolute binding free energy,alchemical,host–guest complexation,OAMe,OctaAcid,SAMPL,SAMPL5}, - file = {JCAM-D-16-00189.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MGTCD94A/JCAM-D-16-00189.pdf:application/pdf} + file = {JCAM-D-16-00189.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MGTCD94A/JCAM-D-16-00189.pdf:application/pdf}, + groups = {OctaAcid} } @article{mock_structure_1986, @@ -695,7 +734,8 @@ @article{mock_structure_1986 year = {1986}, keywords = {CB7,experiment,host–guest complexation}, pages = {4440--4446}, - file = {jo00373a018.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/T42JNGNC/jo00373a018.pdf:application/pdf} + file = {jo00373a018.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/T42JNGNC/jo00373a018.pdf:application/pdf}, + groups = {CB7} } @article{mock_host-guest_1983, @@ -713,11 +753,12 @@ @article{mock_host-guest_1983 year = {1983}, keywords = {CB6,experiment,host–guest complexation}, pages = {3618--3619}, - file = {jo00168a069.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/748M5QX7/jo00168a069.pdf:application/pdf} + file = {jo00168a069.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/748M5QX7/jo00168a069.pdf:application/pdf}, + groups = {CB7} } @article{lee_deciphering_2015, - title = {Deciphering the {{Specific High}}-{{Affinity Binding}} of {{Cucurbit}}[7]uril to {{Amino Acids}} in {{Water}}}, + title = {Deciphering the {{Specific High}}-{{Affinity Binding}} of {{Cucurbit}}[7]Uril to {{Amino Acids}} in {{Water}}}, volume = {119}, issn = {1520-6106, 1520-5207}, doi = {10.1021/acs.jpcb.5b00743}, @@ -731,7 +772,8 @@ @article{lee_deciphering_2015 year = {2015}, keywords = {CB7,experiment,host–guest complexation}, pages = {4628--4636}, - file = {acs%2Ejpcb%2E5b00743.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/9KKGK5NN/acs%2Ejpcb%2E5b00743.pdf:application/pdf} + file = {acs%2Ejpcb%2E5b00743.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/9KKGK5NN/acs%2Ejpcb%2E5b00743.pdf:application/pdf}, + groups = {CB7} } @article{merski_homologous_2015, @@ -751,11 +793,12 @@ @article{merski_homologous_2015 keywords = {conformational change,congeneric series,experiment,homologous series,protein–ligand complexes,T4 lysozyme}, pages = {5039--5044}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/PAEWXHAA/Merski et al. - 2015 - Homologous ligands accommodated by discrete confor.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WUFZNRIX/5039.html:text/html}, + groups = {lysozyme}, pmid = {25847998} } @article{lim_sensitivity_2016, - title = {Sensitivity in Binding Free Energies due to Protein Reorganization}, + title = {Sensitivity in Binding Free Energies Due to Protein Reorganization}, volume = {12}, issn = {1549-9618, 1549-9626}, doi = {10.1021/acs.jctc.6b00532}, @@ -768,7 +811,8 @@ @article{lim_sensitivity_2016 month = jul, year = {2016}, pages = {4620--4631}, - file = {acs%2Ejctc%2E6b00532.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SVUZNG5Q/acs%2Ejctc%2E6b00532.pdf:application/pdf} + file = {acs%2Ejctc%2E6b00532.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SVUZNG5Q/acs%2Ejctc%2E6b00532.pdf:application/pdf}, + groups = {lysozyme} } @article{wang_achieving_2012, @@ -788,6 +832,7 @@ @article{wang_achieving_2012 keywords = {alchemical,binding free energy,drug design,enhanced sampling,lead optimization,protein–ligand binding affinity,structural reorganization,T4 lysozyme}, pages = {1937--1942}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FV2G8P4F/Wang et al. - 2012 - On achieving high accuracy and reliability in the .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QFTW428U/1937.html:text/html}, + groups = {lysozyme,thrombin}, pmid = {22308365} } @@ -806,7 +851,8 @@ @article{khavrutskii_improved_2011 year = {2011}, keywords = {alchemical,binding free energy,Hamiltonian exchange,relative,T4 lysozyme}, pages = {3001--3011}, - file = {ct2003786.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NF5Q89HP/ct2003786.pdf:application/pdf} + file = {ct2003786.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NF5Q89HP/ct2003786.pdf:application/pdf}, + groups = {lysozyme} } @article{gallicchio_binding_2010, @@ -824,7 +870,8 @@ @article{gallicchio_binding_2010 year = {2010}, keywords = {alchemical,BEDAM,binding free energy,L99A,L99A/M102Q,T4 lysozyme}, pages = {2961--2977}, - file = {ct1002913.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SXQ3G6BX/ct1002913.pdf:application/pdf} + file = {ct1002913.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SXQ3G6BX/ct1002913.pdf:application/pdf}, + groups = {lysozyme} } @article{jiang_free_2010, @@ -842,7 +889,8 @@ @article{jiang_free_2010 year = {2010}, keywords = {absolute binding free energy,L99A,lysozyme}, pages = {2559--2565}, - file = {ct1001768.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5REG8HBR/ct1001768.pdf:application/pdf} + file = {ct1001768.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5REG8HBR/ct1001768.pdf:application/pdf}, + groups = {lysozyme} } @article{graves_rescoring_2008, @@ -861,7 +909,8 @@ @article{graves_rescoring_2008 year = {2008}, keywords = {cavity,decoys,experiment,MM–GBSA,molecular docking,T4 lysozyme,virtual screening}, pages = {914--934}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/APD48SID/Graves et al. - 2008 - Rescoring Docking Hit Lists for Model Cavity Sites.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/PXU5DD38/S002228360800096X.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/APD48SID/Graves et al. - 2008 - Rescoring Docking Hit Lists for Model Cavity Sites.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/PXU5DD38/S002228360800096X.html:text/html}, + groups = {lysozyme} } @article{deng_calculation_2006, @@ -880,7 +929,8 @@ @article{deng_calculation_2006 year = {2006}, keywords = {alchemical,binding free energy,L99A,T4 lysozyme}, pages = {1255--1273}, - file = {ct060037v.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2H4ID6DW/ct060037v.pdf:application/pdf} + file = {ct060037v.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2H4ID6DW/ct060037v.pdf:application/pdf}, + groups = {lysozyme} } @article{brenk_probing_2006, @@ -888,7 +938,7 @@ @article{brenk_probing_2006 volume = {357}, issn = {0022-2836}, doi = {10.1016/j.jmb.2006.01.034}, - abstract = {A model binding site was used to investigate charge\textendash{}charge interactions in molecular docking. This simple site, a small (180 \AA{}3) engineered cavity in cyctochrome c peroxidase (CCP), is negatively charged and completely buried from solvent, allowing us to explore the balance between electrostatic energy and ligand desolvation energy in a system where many of the common approximations in docking do not apply. A database with about 5300 molecules was docked into this cavity. Retrospective testing with known ligands and decoys showed that overall the balance between electrostatic interaction and desolvation energy was captured. More interesting were prospective docking scre"ens that looked for novel ligands, especially those that might reveal problems with the docking and energy methods. Based on screens of the 5300 compound database, both high-scoring and low-scoring molecules were acquired and tested for binding. Out of 16 new, high-scoring compounds tested, 15 were observed to bind. All of these were small heterocyclic cations. Binding constants were measured for a few of these, they ranged between 20 $\mu$M and 60 $\mu$M. Crystal structures were determined for ten of these ligands in complex with the protein. The observed ligand geometry corresponded closely to that predicted by docking. Several low-scoring alkyl amino cations were also tested and found to bind. The low docking score of these molecules owed to the relatively high charge density of the charged amino group and the corresponding high desolvation penalty. When the complex structures of those ligands were determined, a bound water molecule was observed interacting with the amino group and a backbone carbonyl group of the cavity. This water molecule mitigates the desolvation penalty and improves the interaction energy relative to that of the ``naked'' site used in the docking screen. Finally, six low-scoring neutral molecules were also tested, with a view to looking for false negative predictions. Whereas most of these did not bind, two did (phenol and 3-fluorocatechol). Crystal structures for these two ligands in complex with the cavity site suggest reasons for their binding. That these neutral molecules do, in fact bind, contradicts previous results in this site and, along with the alkyl amines, provides instructive false negatives that help identify weaknesses in our scoring functions. Several improvements of these are considered.}, + abstract = {A model binding site was used to investigate charge\textendash{}charge interactions in molecular docking. This simple site, a small (180 {\AA}3) engineered cavity in cyctochrome c peroxidase (CCP), is negatively charged and completely buried from solvent, allowing us to explore the balance between electrostatic energy and ligand desolvation energy in a system where many of the common approximations in docking do not apply. A database with about 5300 molecules was docked into this cavity. Retrospective testing with known ligands and decoys showed that overall the balance between electrostatic interaction and desolvation energy was captured. More interesting were prospective docking scre"ens that looked for novel ligands, especially those that might reveal problems with the docking and energy methods. Based on screens of the 5300 compound database, both high-scoring and low-scoring molecules were acquired and tested for binding. Out of 16 new, high-scoring compounds tested, 15 were observed to bind. All of these were small heterocyclic cations. Binding constants were measured for a few of these, they ranged between 20 $\mu$M and 60 $\mu$M. Crystal structures were determined for ten of these ligands in complex with the protein. The observed ligand geometry corresponded closely to that predicted by docking. Several low-scoring alkyl amino cations were also tested and found to bind. The low docking score of these molecules owed to the relatively high charge density of the charged amino group and the corresponding high desolvation penalty. When the complex structures of those ligands were determined, a bound water molecule was observed interacting with the amino group and a backbone carbonyl group of the cavity. This water molecule mitigates the desolvation penalty and improves the interaction energy relative to that of the ``naked'' site used in the docking screen. Finally, six low-scoring neutral molecules were also tested, with a view to looking for false negative predictions. Whereas most of these did not bind, two did (phenol and 3-fluorocatechol). Crystal structures for these two ligands in complex with the cavity site suggest reasons for their binding. That these neutral molecules do, in fact bind, contradicts previous results in this site and, along with the alkyl amines, provides instructive false negatives that help identify weaknesses in our scoring functions. Several improvements of these are considered.}, timestamp = {2016-08-15T19:01:55Z}, number = {5}, urldate = {2016-08-15}, @@ -898,7 +948,8 @@ @article{brenk_probing_2006 year = {2006}, keywords = {CCP,cyctochrome c peroxidase,electrostatic,experiment,molecular docking,solvation,X-ray crystallography}, pages = {1449--1470}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/W87KQGN3/Brenk et al. - 2006 - Probing Molecular Docking in a Charged Model Bindi.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/JT2DVNTS/S0022283606000623.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/W87KQGN3/Brenk et al. - 2006 - Probing Molecular Docking in a Charged Model Bindi.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/JT2DVNTS/S0022283606000623.html:text/html}, + groups = {CCP} } @article{graves_decoys_2005, @@ -916,7 +967,8 @@ @article{graves_decoys_2005 year = {2005}, keywords = {experiment,T4 lysozyme}, pages = {3714--3728}, - file = {jm0491187.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7INK6MM9/jm0491187.pdf:application/pdf} + file = {jm0491187.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7INK6MM9/jm0491187.pdf:application/pdf}, + groups = {lysozyme} } @article{boresch_absolute_2003, @@ -935,7 +987,8 @@ @article{boresch_absolute_2003 year = {2003}, keywords = {alchemical,binding free energy,L99A,T4 lysozyme}, pages = {9535--9551}, - file = {jp0217839.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RRNU8KGN/jp0217839.pdf:application/pdf} + file = {jp0217839.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RRNU8KGN/jp0217839.pdf:application/pdf}, + groups = {lysozyme} } @article{wei_model_2002, @@ -944,7 +997,7 @@ @article{wei_model_2002 issn = {0022-2836}, doi = {10.1016/S0022-2836(02)00777-5}, abstract = {Prediction of interaction energies between ligands and their receptors remains a major challenge for structure-based inhibitor discovery. Much effort has been devoted to developing scoring schemes that can successfully rank the affinities of a diverse set of possible ligands to a binding site for which the structure is known. To test these scoring functions, well-characterized experimental systems can be very useful. Here, mutation-created binding sites in T4 lysozyme were used to investigate how the quality of atomic charges and solvation energies affects molecular docking. Atomic charges and solvation energies were calculated for 172,118 molecules in the Available Chemicals Directory using a semi-empirical quantum mechanical approach by the program AMSOL\textdagger\textdagger{}http://t1.chem.umn.edu/amsol -. The database was first screened against the apolar cavity site created by the mutation Leu99$\rightarrow$Ala (L99A). Compared to the electronegativity-based charges that are widely used, the new charges and desolvation energies improved ranking of known apolar ligands, and better distinguished them from more polar isosteres that are not observed to bind. To investigate whether the new charges had predictive value, the non-polar residue Met102, which forms part of the binding site, was changed to the polar residue glutamine. The structure of the resulting Leu99$\rightarrow$Ala and Met102$\rightarrow$Gln double mutant of T4 lysozyme (L99A/M102Q) was determined and the docking calculation was repeated for the new site. Seven representative polar molecules that preferentially docked to the polar versus the apolar binding site were tested experimentally. All seven bind to the polar cavity (L99A/M102Q) but do not detectably bind to the apolar cavity (L99A). Five ligand-bound structures of L99A/M102Q were determined by X-ray crystallography. Docking predictions corresponded to the crystallographic results to within 0.4 \AA{} RMSD. Improved treatment of partial atomic charges and desolvation energies in database docking appears feasible and leads to better distinction of true ligands. Simple model binding sites, such as L99A and its more polar variants, may find broad use in the development and testing of docking algorithms.}, +. The database was first screened against the apolar cavity site created by the mutation Leu99$\rightarrow$Ala (L99A). Compared to the electronegativity-based charges that are widely used, the new charges and desolvation energies improved ranking of known apolar ligands, and better distinguished them from more polar isosteres that are not observed to bind. To investigate whether the new charges had predictive value, the non-polar residue Met102, which forms part of the binding site, was changed to the polar residue glutamine. The structure of the resulting Leu99$\rightarrow$Ala and Met102$\rightarrow$Gln double mutant of T4 lysozyme (L99A/M102Q) was determined and the docking calculation was repeated for the new site. Seven representative polar molecules that preferentially docked to the polar versus the apolar binding site were tested experimentally. All seven bind to the polar cavity (L99A/M102Q) but do not detectably bind to the apolar cavity (L99A). Five ligand-bound structures of L99A/M102Q were determined by X-ray crystallography. Docking predictions corresponded to the crystallographic results to within 0.4 {\AA} RMSD. Improved treatment of partial atomic charges and desolvation energies in database docking appears feasible and leads to better distinction of true ligands. Simple model binding sites, such as L99A and its more polar variants, may find broad use in the development and testing of docking algorithms.}, timestamp = {2016-08-15T19:06:59Z}, number = {2}, urldate = {2016-08-15}, @@ -954,7 +1007,8 @@ @article{wei_model_2002 year = {2002}, keywords = {atomic charge,experiment,L99A/M102Q,molecular docking,solvation,T4 lysozyme,X-ray crystallography}, pages = {339--355}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/JSG6JI8S/Wei et al. - 2002 - A Model Binding Site for Testing Scoring Functions.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/K2ME5AVG/S0022283602007775.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/JSG6JI8S/Wei et al. - 2002 - A Model Binding Site for Testing Scoring Functions.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/K2ME5AVG/S0022283602007775.html:text/html}, + groups = {lysozyme} } @article{morton_specificity_1995, @@ -973,7 +1027,8 @@ @article{morton_specificity_1995 year = {1995}, keywords = {experiment,L99A,lysozyme}, pages = {8576--8588}, - file = {bi00027a007.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2BW9ASID/bi00027a007.pdf:application/pdf} + file = {bi00027a007.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2BW9ASID/bi00027a007.pdf:application/pdf}, + groups = {lysozyme} } @article{morton_energetic_1995, @@ -991,7 +1046,8 @@ @article{morton_energetic_1995 year = {1995}, keywords = {experiment,L99A,lysozyme}, pages = {8564--8575}, - file = {bi00027a006.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FBIEIH5V/bi00027a006.pdf:application/pdf} + file = {bi00027a006.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FBIEIH5V/bi00027a006.pdf:application/pdf}, + groups = {lysozyme} } @article{wang_identifying_2013, @@ -1010,7 +1066,8 @@ @article{wang_identifying_2013 year = {2013}, keywords = {alchemical,binding free energy,T4 lysozyme}, pages = {989--1007}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/VBPDHJWW/Wang et al. - 2013 - Identifying ligand binding sites and poses using G.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HG8A5TVT/10.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/VBPDHJWW/Wang et al. - 2013 - Identifying ligand binding sites and poses using G.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HG8A5TVT/10.html:text/html}, + groups = {lysozyme} } @article{wang_itc_2016, @@ -1028,7 +1085,8 @@ @article{wang_itc_2016 year = {2016}, keywords = {experiment,host–guest complexation,OctaAcid,pKa}, pages = {84--90}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SXKXZ9H7/Wang et al. - 2016 - ITC and NMR analysis of the encapsulation of fatty.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/PAMT3ERA/10610278.2015.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SXKXZ9H7/Wang et al. - 2016 - ITC and NMR analysis of the encapsulation of fatty.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/PAMT3ERA/10610278.2015.html:text/html}, + groups = {OctaAcid} } @article{boyce_predicting_2009, @@ -1044,7 +1102,8 @@ @article{boyce_predicting_2009 year = {2009}, keywords = {alchemical,binding free energy,T4 lysozyme}, pages = {747--763}, - file = {Boyce_2009-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DSMXQW7B/Boyce_2009-J. Mol. Biol.pdf:application/pdf;Boyce_2009-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V76QVXMJ/Boyce_2009-J. Mol. Biol.pdf:application/pdf} + file = {Boyce_2009-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DSMXQW7B/Boyce_2009-J. Mol. Biol.pdf:application/pdf;Boyce_2009-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V76QVXMJ/Boyce_2009-J. Mol. Biol.pdf:application/pdf}, + groups = {lysozyme} } @article{chodera_alchemical_2011, @@ -1101,7 +1160,8 @@ @article{mobley_use_2006 year = {2006}, keywords = {alchemical,binding free energy,T4 lysozyme}, pages = {084902}, - file = {Mobley_2006-J. Chem. Phys:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/GTZWQ4SB/Mobley_2006-J. Chem. Phys.pdf:application/pdf;Mobley_2006-J. Chem. Phys:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q7VCT8E7/Mobley_2006-J. Chem. Phys.pdf:application/pdf} + file = {Mobley_2006-J. Chem. Phys:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/GTZWQ4SB/Mobley_2006-J. Chem. Phys.pdf:application/pdf;Mobley_2006-J. Chem. Phys:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q7VCT8E7/Mobley_2006-J. Chem. Phys.pdf:application/pdf}, + groups = {lysozyme} } @article{mobley_confine_2007, @@ -1117,7 +1177,8 @@ @article{mobley_confine_2007 year = {2007}, keywords = {alchemical,binding free energy,T4 lysozyme}, pages = {1231--1235}, - file = {Mobley_2007-J Chem Theory Comput-3:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ATW4GQEX/Mobley_2007-J Chem Theory Comput-3.pdf:application/pdf;Mobley_2007-J Chem Theory Comput-3:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WPM8VQFJ/Mobley_2007-J Chem Theory Comput-3.pdf:application/pdf} + file = {Mobley_2007-J Chem Theory Comput-3:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ATW4GQEX/Mobley_2007-J Chem Theory Comput-3.pdf:application/pdf;Mobley_2007-J Chem Theory Comput-3:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WPM8VQFJ/Mobley_2007-J Chem Theory Comput-3.pdf:application/pdf}, + groups = {lysozyme} } @article{mobley_predicting_2007, @@ -1133,7 +1194,8 @@ @article{mobley_predicting_2007 year = {2007}, keywords = {alchemical,binding free energy,T4 lysozyme}, pages = {1118--1134}, - file = {Mobley_2007-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UGWUB2N9/Mobley_2007-J. Mol. Biol.pdf:application/pdf;Mobley_2007-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WA4AJ6R7/Mobley_2007-J. Mol. Biol.pdf:application/pdf} + file = {Mobley_2007-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UGWUB2N9/Mobley_2007-J. Mol. Biol.pdf:application/pdf;Mobley_2007-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WA4AJ6R7/Mobley_2007-J. Mol. Biol.pdf:application/pdf}, + groups = {lysozyme} } @article{mobley_perspective_2012, @@ -1162,7 +1224,8 @@ @article{muddana_sampl4_2014 year = {2014}, keywords = {alchemical,CB7,cucurbituril,host–guest complexation,OctaAcid,overview,SAMPL,SAMPL4}, pages = {305--317}, - file = {Muddana_2014-J Comput Aided Mol Des:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FG5FXVAS/Muddana_2014-J Comput Aided Mol Des.pdf:application/pdf;Muddana_2014-J Comput Aided Mol Des:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QAVCZ38I/Muddana_2014-J Comput Aided Mol Des.pdf:application/pdf} + file = {Muddana_2014-J Comput Aided Mol Des:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FG5FXVAS/Muddana_2014-J Comput Aided Mol Des.pdf:application/pdf;Muddana_2014-J Comput Aided Mol Des:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QAVCZ38I/Muddana_2014-J Comput Aided Mol Des.pdf:application/pdf}, + groups = {CB7,MKG,OctaAcid} } @article{reif_net_2014, @@ -1196,7 +1259,8 @@ @article{rocklin_blind_2013 year = {2013}, keywords = {alchemical,binding free energy,CCP,CCP closed,CCP open}, pages = {4569--4583}, - file = {Rocklin_2013-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q7P86U47/Rocklin_2013-J. Mol. Biol.pdf:application/pdf} + file = {Rocklin_2013-J. Mol. Biol:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q7P86U47/Rocklin_2013-J. Mol. Biol.pdf:application/pdf}, + groups = {CCP} } @misc{docker_what_2015, @@ -1252,7 +1316,8 @@ @article{Shirts:2007:JPhysChemB month = nov, year = {2007}, pages = {13052--13063}, - file = {Shirts_2007-J Phys Chem B:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/EJE22ZBD/Shirts_2007-J Phys Chem B.pdf:application/pdf;Shirts_2007-J Phys Chem B:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RDQ54MHR/Shirts_2007-J Phys Chem B.pdf:application/pdf} + file = {Shirts_2007-J Phys Chem B:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/EJE22ZBD/Shirts_2007-J Phys Chem B.pdf:application/pdf;Shirts_2007-J Phys Chem B:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RDQ54MHR/Shirts_2007-J Phys Chem B.pdf:application/pdf}, + groups = {lysozyme} } @incollection{shirts_introduction_2013, @@ -1279,7 +1344,8 @@ @article{schrodinger_accurate_2015 year = {2015}, keywords = {alchemical,relative free energy,thrombin}, pages = {2695--2703}, - file = {Wang_2015-J Am Chem Soc:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3DMV4H3M/Wang_2015-J Am Chem Soc.pdf:application/pdf;Wang_2015-J Am Chem Soc:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/GKI3EQMH/Wang_2015-J Am Chem Soc.pdf:application/pdf} + file = {Wang_2015-J Am Chem Soc:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3DMV4H3M/Wang_2015-J Am Chem Soc.pdf:application/pdf;Wang_2015-J Am Chem Soc:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/GKI3EQMH/Wang_2015-J Am Chem Soc.pdf:application/pdf}, + groups = {thrombin} } @misc{isaacs_personal_2016, @@ -1304,6 +1370,7 @@ @article{shirts_statistically_2008 year = {2008}, keywords = {logP Paper,SAMPL5}, pages = {124105}, + file = {172E1FD3-4E87-484C-97ED-F53BF3E4F962.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/4XICNNEU/172E1FD3-4E87-484C-97ED-F53BF3E4F962.pdf:application/pdf}, pmid = {19045004}, pmcid = {PMC2671659} } @@ -1322,7 +1389,7 @@ @article{liu_using_2016 year = {2016}, keywords = {alchemical,solubility}, pages = {1930--1941}, - file = {BC07EF9F-01AE-4D64-BA82-863FA1A20E49.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/6XJNH7F9/BC07EF9F-01AE-4D64-BA82-863FA1A20E49.pdf:application/pdf}, + file = {acs%2Ejctc%2E5b00934.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/342QE3AS/acs%2Ejctc%2E5b00934.pdf:application/pdf}, pmid = {26878198} } @@ -1340,7 +1407,8 @@ @article{sullivan_binding_2016 year = {2016}, keywords = {experiment,OctaAcid,SAMPL,SAMPL5}, pages = {1--8}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DZECQZV7/Sullivan et al. - 2016 - Binding of carboxylate and trimethylammonium salts.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AZS2AFW7/10.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DZECQZV7/Sullivan et al. - 2016 - Binding of carboxylate and trimethylammonium salts.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AZS2AFW7/10.html:text/html}, + groups = {OctaAcid} } @article{lee_permeability_2016, @@ -1374,7 +1442,8 @@ @article{calabro_elucidation_2016 month = jun, year = {2016}, keywords = {alchemical,thrombin}, - file = {acs%2Ejpcb%2E6b03296.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/D5ZBGTND/acs%2Ejpcb%2E6b03296.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/6ZAN6CKH/acs.jpcb.html:text/html} + file = {acs%2Ejpcb%2E6b03296.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/D5ZBGTND/acs%2Ejpcb%2E6b03296.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/6ZAN6CKH/acs.jpcb.html:text/html}, + groups = {thrombin} } @article{comer_permeability_2014, @@ -1425,14 +1494,15 @@ @article{rekharsky_synthetic_2007 keywords = {CB7,cucurbituril,entropy control,ferrocene derivatives,host–guest complexation,Thermodynamics}, pages = {20737--20742}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FBXVGGQ2/Rekharsky et al. - 2007 - A synthetic host-guest system achieves avidin-biot.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2F966URP/20737.html:text/html}, + groups = {CB7}, pmid = {18093926} } @article{liu_cucurbituril_2005, - title = {The {{Cucurbit}}[n]uril {{Family}}: {{Prime Components}} for {{Self}}-{{Sorting Systems}}}, + title = {The {{Cucurbit}}[n]Uril {{Family}}: {{Prime Components}} for {{Self}}-{{Sorting Systems}}}, volume = {127}, issn = {0002-7863, 1520-5126}, - shorttitle = {The {{Cucurbit}}[ {\emph{N}} ]Uril {{Family}}}, + shorttitle = {The {{Cucurbit}}[ {\emph{n}} ]Uril {{Family}}}, doi = {10.1021/ja055013x}, language = {en}, timestamp = {2016-07-20T18:10:51Z}, @@ -1444,7 +1514,8 @@ @article{liu_cucurbituril_2005 year = {2005}, keywords = {CB7,cucurbituril,host–guest complexation}, pages = {15959--15967}, - file = {ja055013x.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q69GH3N7/ja055013x.pdf:application/pdf} + file = {ja055013x.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q69GH3N7/ja055013x.pdf:application/pdf}, + groups = {CB7} } @article{muddana_sampl3_2012, @@ -1464,7 +1535,8 @@ @article{muddana_sampl3_2012 year = {2012}, keywords = {alchemical,CB7,cucurbituril,host–guest complexation,overview,SAMPL,SAMPL3}, pages = {475--487}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QPWKPVRN/Muddana et al. - 2012 - Blind prediction of host–guest binding affinities.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZUQH39X3/10.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QPWKPVRN/Muddana et al. - 2012 - Blind prediction of host–guest binding affinities.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZUQH39X3/10.html:text/html}, + groups = {CB7} } @article{rogers_role_2013, @@ -1482,7 +1554,8 @@ @article{rogers_role_2013 year = {2013}, keywords = {alchemical,CB7,cucurbituril,host–guest complexation,thermodynamic integration}, pages = {46--53}, - file = {ct300515n.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/S3KDDPTV/ct300515n.pdf:application/pdf} + file = {ct300515n.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/S3KDDPTV/ct300515n.pdf:application/pdf}, + groups = {CB7} } @article{kantonen_evaluation_2016, @@ -1605,7 +1678,7 @@ @article{leonis_contribution_2013 } @article{mobley_proposal_2015, - title = {A Proposal for Regularly Updated Review/Survey articles: "{{Perpetual Reviews}}"}, + title = {A Proposal for Regularly Updated Review/Survey Articles: "{{Perpetual Reviews}}"}, shorttitle = {A Proposal for Regularly Updated Review/Survey Articles}, abstract = {We advocate the publication of review/survey articles that will be updated regularly, both in traditional journals and novel venues. We call these "perpetual reviews." This idea naturally builds on the dissemination and archival capabilities present in the modern internet, and indeed perpetual reviews exist already in some forms. Perpetual review articles allow authors to maintain over time the relevance of non-research scholarship that requires a significant investment of effort. Further, such reviews published in a purely electronic format without space constraints can also permit more pedagogical scholarship and clearer treatment of technical issues that remain obscure in a brief treatment.}, timestamp = {2016-08-30T00:09:55Z}, @@ -1640,15 +1713,16 @@ @article{mosca_preparative_2016 year = {2016}, keywords = {Chemical biology,Chemical synthesis,Organic chemistry,Supramolecular chemistry}, pages = {1371--1387}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5XNSIK87/Mosca et al. - 2016 - Preparative scale and convenient synthesis of a wa.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/67QCGQG4/nprot.2016.078.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5XNSIK87/Mosca et al. - 2016 - Preparative scale and convenient synthesis of a wa.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/67QCGQG4/nprot.2016.078.html:text/html}, + groups = {OctaAcid} } @article{cao_attomolar_2014, - title = {Cucurbit[7]uril$\cdot${{Guest Pair}} with an {{Attomolar Dissociation Constant}}}, + title = {Cucurbit[7]Uril$\cdot${{Guest Pair}} with an {{Attomolar Dissociation Constant}}}, volume = {53}, issn = {1521-3773}, doi = {10.1002/anie.201309635}, - abstract = {Host$\cdot$guest complexes between cucurbit[7] (CB[7]) or CB[8] and diamantane diammonium ion guests 3 or 6 were studied by 1H\hspace{0.25em}NMR spectroscopy and X-ray crystallography. 1H\hspace{0.25em}NMR competition experiments revealed that CB[7]$\cdot$6 is among the tightest monovalent non-covalent complexes ever reported in water with Ka=7.2\texttimes{}1017\,M-1 in pure D2O and 1.9\texttimes{}1015\,M-1 in D2O buffered with NaO2CCD3 (50\hspace{0.25em}mM). The crystal structure of CB[7]$\cdot$6 allowed us to identify some of the structural features responsible for the ultratight binding, including the distance between the NMe3+ groups of 6 (7.78\hspace{0.25em}\AA), which allows it to establish 14 optimal ion-dipole interactions with CB[7], the complementarity of the convex van der Waals surface contours of 6 with the corresponding concave surfaces of CB[7], desolvation of the CO portals within the CB[7]$\cdot$6 complex, and the co-linearity of the C7\hspace{0.25em}axis of CB[7] with the N+$\cdot\cdot\cdot$N+ line in 6. This work further blurs the lines of distinction between natural and synthetic receptors.}, + abstract = {Host$\cdot$guest complexes between cucurbit[7] (CB[7]) or CB[8] and diamantane diammonium ion guests 3 or 6 were studied by 1H\hspace{0.25em}NMR spectroscopy and X-ray crystallography. 1H\hspace{0.25em}NMR competition experiments revealed that CB[7]$\cdot$6 is among the tightest monovalent non-covalent complexes ever reported in water with Ka=7.2\texttimes{}1017\,M-1 in pure D2O and 1.9\texttimes{}1015\,M-1 in D2O buffered with NaO2CCD3 (50\hspace{0.25em}mM). The crystal structure of CB[7]$\cdot$6 allowed us to identify some of the structural features responsible for the ultratight binding, including the distance between the NMe3+ groups of 6 (7.78\hspace{0.25em}{\AA}), which allows it to establish 14 optimal ion-dipole interactions with CB[7], the complementarity of the convex van der Waals surface contours of 6 with the corresponding concave surfaces of CB[7], desolvation of the CO portals within the CB[7]$\cdot$6 complex, and the co-linearity of the C7\hspace{0.25em}axis of CB[7] with the N+$\cdot\cdot\cdot$N+ line in 6. This work further blurs the lines of distinction between natural and synthetic receptors.}, language = {en}, timestamp = {2016-09-01T19:22:15Z}, number = {4}, @@ -1659,14 +1733,15 @@ @article{cao_attomolar_2014 year = {2014}, keywords = {affinity pairs,avidin–biotin,CB7,cucurbit[n]uril,experiment,host–guest complexation,host-guest systems,X-ray diffraction}, pages = {988--993}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FNHB6VJ4/Cao et al. - 2014 - Cucurbit[7]uril⋅Guest Pair with an Attomolar Disso.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CBJSPQSX/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FNHB6VJ4/Cao et al. - 2014 - Cucurbit[7]uril⋅Guest Pair with an Attomolar Disso.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CBJSPQSX/abstract.html:text/html}, + groups = {CB7} } @article{Jang:2014:Angew.Chem.Int.Ed., - title = {Cucurbit[7]uril: {{A High}}-{{Affinity Host}} for {{Encapsulation}} of {{Amino Saccharides}} and {{Supramolecular Stabilization}} of {{Their}} $\alpha$-{{Anomers}} in {{Water}}}, + title = {Cucurbit[7]Uril: {{A High}}-{{Affinity Host}} for {{Encapsulation}} of {{Amino Saccharides}} and {{Supramolecular Stabilization}} of {{Their}} $\alpha$-{{Anomers}} in {{Water}}}, volume = {53}, issn = {1521-3773}, - shorttitle = {Cucurbit[7]uril}, + shorttitle = {Cucurbit[7]Uril}, doi = {10.1002/anie.201308879}, abstract = {Cucurbit[7]uril (CB[7]), an uncharged and water-soluble macrocyclic host, binds protonated amino saccharides (D-glucosamine, D-galactosamine, D-mannosamine and 6-amino-6-deoxy-D-glucose) with excellent affinity (Ka=103 to 104\,M-1). The host\textendash{}guest complexation was confirmed by NMR spectroscopy, isothermal titration calorimetry (ITC), and MALDI-TOF mass spectral analyses. NMR analyses revealed that the amino saccharides, except D-mannosamine, are bound as $\alpha$-anomers within the CB[7] cavity. ITC analyses reveal that CB[7] has excellent affinity for binding amino saccharides in water. The maximum affinity was observed for D-galactosamine hydrochloride (Ka=1.6\texttimes{}104\,M-1). Such a strong affinity for any saccharide in water using a synthetic receptor is unprecedented, as is the supramolecular stabilization of an $\alpha$-anomer by the host.}, language = {en}, @@ -1679,7 +1754,8 @@ @article{Jang:2014:Angew.Chem.Int.Ed. year = {2014}, keywords = {calorimetry,CB7,experiment,host–guest complexation,host-guest systems,hydrophobic effect,molecular recognition,NMR spectroscopy}, pages = {1003--1007}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/W7V9ERP5/Jang et al. - 2014 - Cucurbit[7]uril A High-Affinity Host for Encapsul.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/D3RUUMFU/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/W7V9ERP5/Jang et al. - 2014 - Cucurbit[7]uril A High-Affinity Host for Encapsul.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/D3RUUMFU/abstract.html:text/html}, + groups = {CB7} } @article{su_docking_2001, @@ -1699,7 +1775,8 @@ @article{su_docking_2001 year = {2001}, keywords = {affinity,database,diversity,docking,experiment,inhibitor design,inhibitor discovery,L99A,screening}, pages = {279--293}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BPMA9RK5/Su et al. - 2001 - Docking molecules by families to increase the dive.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/49AJ7FPS/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BPMA9RK5/Su et al. - 2001 - Docking molecules by families to increase the dive.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/49AJ7FPS/abstract.html:text/html}, + groups = {lysozyme} } @article{hillyer_synthesis_2016, @@ -1716,7 +1793,8 @@ @article{hillyer_synthesis_2016 month = aug, year = {2016}, pages = {4048--4051}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/B95HCATA/Hillyer et al. - 2016 - Synthesis of Water-Soluble Deep-Cavity Cavitands.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/X4MTSCZQ/acs.orglett.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/B95HCATA/Hillyer et al. - 2016 - Synthesis of Water-Soluble Deep-Cavity Cavitands.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/X4MTSCZQ/acs.orglett.html:text/html}, + groups = {OctaAcid} } @article{wei_testing_2004, @@ -1724,7 +1802,7 @@ @article{wei_testing_2004 volume = {337}, issn = {0022-2836}, doi = {10.1016/j.jmb.2004.02.015}, - abstract = {Sampling receptor flexibility is challenging for database docking. We consider a method that treats multiple flexible regions of the binding site independently, recombining them to generate different discrete conformations. This algorithm scales linearly rather than exponentially with the receptor's degrees of freedom. The method was first evaluated for its ability to identify known ligands of a hydrophobic cavity mutant of T4 lysozyme (L99A). Some 200,000 molecules of the Available Chemical Directory (ACD) were docked against an ensemble of cavity conformations. Surprisingly, the enrichment of known ligands from among a much larger number of decoys in the ACD was worse than simply docking to the apo conformation alone. Large decoys, accommodated in the larger cavity conformations sampled in the ensemble, were ranked better than known small ligands. The calculation was redone with an energy correction term that considered the cost of forming the larger cavity conformations. Enrichment improved, as did the balance between high-ranking large and small ligands. In a second retrospective test, the ACD was docked against a conformational ensemble of thymidylate synthase. Compared to docking against individual enzyme conformations, the flexible receptor docking approach improved enrichment of known ligands. Including a receptor conformational energy weighting term improved enrichment further. To test the method prospectively, the ACD database was docked against another cavity mutant of lysozyme (L99A/M102Q). A total of 18 new compounds predicted to bind this polar cavity and to change its conformation were tested experimentally; 14 were found to bind. The bound structures for seven ligands were determined by X-ray crystallography. The predicted geometries of these ligands all corresponded to the observed geometries to within 0.7 \AA{} RMSD or better. Significant conformational changes of the cavity were observed in all seven complexes. In five structures, part of the observed accommodations were correctly predicted; in two structures, the receptor conformational changes were unanticipated and thus never sampled. These results suggest that although sampling receptor flexibility can lead to novel ligands that would have been missed when docking a rigid structure, it is also important to consider receptor conformational energy.}, + abstract = {Sampling receptor flexibility is challenging for database docking. We consider a method that treats multiple flexible regions of the binding site independently, recombining them to generate different discrete conformations. This algorithm scales linearly rather than exponentially with the receptor's degrees of freedom. The method was first evaluated for its ability to identify known ligands of a hydrophobic cavity mutant of T4 lysozyme (L99A). Some 200,000 molecules of the Available Chemical Directory (ACD) were docked against an ensemble of cavity conformations. Surprisingly, the enrichment of known ligands from among a much larger number of decoys in the ACD was worse than simply docking to the apo conformation alone. Large decoys, accommodated in the larger cavity conformations sampled in the ensemble, were ranked better than known small ligands. The calculation was redone with an energy correction term that considered the cost of forming the larger cavity conformations. Enrichment improved, as did the balance between high-ranking large and small ligands. In a second retrospective test, the ACD was docked against a conformational ensemble of thymidylate synthase. Compared to docking against individual enzyme conformations, the flexible receptor docking approach improved enrichment of known ligands. Including a receptor conformational energy weighting term improved enrichment further. To test the method prospectively, the ACD database was docked against another cavity mutant of lysozyme (L99A/M102Q). A total of 18 new compounds predicted to bind this polar cavity and to change its conformation were tested experimentally; 14 were found to bind. The bound structures for seven ligands were determined by X-ray crystallography. The predicted geometries of these ligands all corresponded to the observed geometries to within 0.7 {\AA} RMSD or better. Significant conformational changes of the cavity were observed in all seven complexes. In five structures, part of the observed accommodations were correctly predicted; in two structures, the receptor conformational changes were unanticipated and thus never sampled. These results suggest that although sampling receptor flexibility can lead to novel ligands that would have been missed when docking a rigid structure, it is also important to consider receptor conformational energy.}, timestamp = {2016-08-31T19:58:29Z}, number = {5}, urldate = {2016-08-31}, @@ -1734,7 +1812,8 @@ @article{wei_testing_2004 year = {2004}, keywords = {binding free energy,conformational energy,induced fit,L99A/M102Q,molecular docking,T4 lysozyme,X-ray crystallography}, pages = {1161--1182}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZZS82ARK/Wei et al. - 2004 - Testing a Flexible-receptor Docking Algorithm in a.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MKSMHHTU/S0022283604001718.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZZS82ARK/Wei et al. - 2004 - Testing a Flexible-receptor Docking Algorithm in a.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MKSMHHTU/S0022283604001718.html:text/html}, + groups = {lysozyme} } @article{banba_efficient_2000, @@ -1752,7 +1831,8 @@ @article{banba_efficient_2000 year = {2000}, keywords = {alchemical,binding free energy,CCP,CCP closed,closed}, pages = {6903--6910}, - file = {jp001177i.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/X2CGRVG9/jp001177i.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/GKCWZ3VC/jp001177i.html:text/html} + file = {jp001177i.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/X2CGRVG9/jp001177i.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/GKCWZ3VC/jp001177i.html:text/html}, + groups = {CCP} } @article{banba_free_2000, @@ -1770,7 +1850,8 @@ @article{banba_free_2000 year = {2000}, keywords = {binding free energy,Cavitation,CCP,CCP closed,closed,Entropy,Free energy,Physics demonstrations,Proteins}, pages = {3423--3433}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/M9EMDU39/Banba and Iii - 2000 - Free energy screening of small ligands binding to .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3T43FFHK/1.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/M9EMDU39/Banba and Iii - 2000 - Free energy screening of small ligands binding to .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3T43FFHK/1.html:text/html}, + groups = {CCP} } @article{rosenfeld_excision_2002, @@ -1789,11 +1870,12 @@ @article{rosenfeld_excision_2002 year = {2002}, keywords = {CCP,CCP open,electron transfer,ligand binding,protein cavities,Protein engineering,W191G}, pages = {1251--1259}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q5H2BK6T/Rosenfeld et al. - 2002 - Excision of a proposed electron transfer pathway i.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/F7ZVW9NJ/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Q5H2BK6T/Rosenfeld et al. - 2002 - Excision of a proposed electron transfer pathway i.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/F7ZVW9NJ/abstract.html:text/html}, + groups = {CCP} } @article{musah_artificial_2002, - title = {Artificial Protein Cavities as Specific Ligand-Binding Templates: Characterization of an Engineered Heterocyclic Cation-Binding Site That Preserves the Evolved Specificity of the Parent protein1}, + title = {Artificial Protein Cavities as Specific Ligand-Binding Templates: Characterization of an Engineered Heterocyclic Cation-Binding Site That Preserves the Evolved Specificity of the Parent Protein1}, volume = {315}, issn = {0022-2836}, shorttitle = {Artificial Protein Cavities as Specific Ligand-Binding Templates}, @@ -1808,7 +1890,8 @@ @article{musah_artificial_2002 year = {2002}, keywords = {cavity complementation,cavity mutant,CCP,CCP open,chemical rescue,Protein engineering,protein-ligand binding,W191G}, pages = {845--857}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V3KJS3UN/Musah et al. - 2002 - Artificial protein cavities as specific ligand-bin.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WIS78GVA/S0022283601952878.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V3KJS3UN/Musah et al. - 2002 - Artificial protein cavities as specific ligand-bin.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WIS78GVA/S0022283601952878.html:text/html}, + groups = {CCP} } @article{fitzgerald_ligand-gated_1996, @@ -1827,7 +1910,8 @@ @article{fitzgerald_ligand-gated_1996 year = {1996}, keywords = {CCP,CCP closed}, pages = {626--631}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FSAJM8VX/Fitzgerald et al. - 1996 - A ligand-gated, hinged loop rearrangement opens a .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Z5FD6SEX/nsb0796-626.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FSAJM8VX/Fitzgerald et al. - 1996 - A ligand-gated, hinged loop rearrangement opens a .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/Z5FD6SEX/nsb0796-626.html:text/html}, + groups = {CCP} } @article{mikulskis_large-scale_2014, @@ -1835,7 +1919,7 @@ @article{mikulskis_large-scale_2014 volume = {54}, issn = {1549-9596}, doi = {10.1021/ci5004027}, - abstract = {We have performed a large-scale test of alchemical perturbation calculations with the Bennett acceptance-ratio (BAR) approach to estimate relative affinities for the binding of 107 ligands to 10 different proteins. Employing 20-\AA{} truncated spherical systems and only one intermediate state in the perturbations, we obtain an error of less than 4 kJ/mol for 54\% of the studied relative affinities and a precision of 0.5 kJ/mol on average. However, only four of the proteins gave acceptable errors, correlations, and rankings. The results could be improved by using nine intermediate states in the simulations or including the entire protein in the simulations using periodic boundary conditions. However, 27 of the calculated affinities still gave errors of more than 4 kJ/mol, and for three of the proteins the results were not satisfactory. This shows that the performance of BAR calculations depends on the target protein and that several transformations gave poor results owing to limitations in the molecular-mechanics force field or the restricted sampling possible within a reasonable simulation time. Still, the BAR results are better than docking calculations for most of the proteins.}, + abstract = {We have performed a large-scale test of alchemical perturbation calculations with the Bennett acceptance-ratio (BAR) approach to estimate relative affinities for the binding of 107 ligands to 10 different proteins. Employing 20-{\AA} truncated spherical systems and only one intermediate state in the perturbations, we obtain an error of less than 4 kJ/mol for 54\% of the studied relative affinities and a precision of 0.5 kJ/mol on average. However, only four of the proteins gave acceptable errors, correlations, and rankings. The results could be improved by using nine intermediate states in the simulations or including the entire protein in the simulations using periodic boundary conditions. However, 27 of the calculated affinities still gave errors of more than 4 kJ/mol, and for three of the proteins the results were not satisfactory. This shows that the performance of BAR calculations depends on the target protein and that several transformations gave poor results owing to limitations in the molecular-mechanics force field or the restricted sampling possible within a reasonable simulation time. Still, the BAR results are better than docking calculations for most of the proteins.}, timestamp = {2016-08-31T23:04:40Z}, number = {10}, urldate = {2016-08-31}, @@ -1881,7 +1965,8 @@ @article{baum_non-additivity_2010 year = {2010}, keywords = {crystal structure analysis,isothermal titration calorimetry,ligand–protein interactions,non-additivity of functional group contributions,thrombin}, pages = {1042--1054}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/F2Z8DAU8/Baum et al. - 2010 - Non-additivity of Functional Group Contributions i.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7I6QIE7B/S0022283610001622.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/F2Z8DAU8/Baum et al. - 2010 - Non-additivity of Functional Group Contributions i.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7I6QIE7B/S0022283610001622.html:text/html}, + groups = {thrombin} } @article{plattner_protein_2015, @@ -1897,7 +1982,8 @@ @article{plattner_protein_2015 year = {2015}, keywords = {alchemical,binding free energy,MSM,trypsin}, pages = {7653}, - file = {ncomms8653.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UW9KSKZG/ncomms8653.pdf:application/pdf} + file = {ncomms8653.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UW9KSKZG/ncomms8653.pdf:application/pdf}, + groups = {trypsin} } @article{talhout_understanding_2003, @@ -1915,7 +2001,8 @@ @article{talhout_understanding_2003 month = sep, year = {2003}, pages = {10570--10579}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/T9PAKZ3D/Talhout et al. - 2003 - Understanding Binding Affinity A Combined Isothe.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/4VVF6T7F/ja034676g.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/T9PAKZ3D/Talhout et al. - 2003 - Understanding Binding Affinity A Combined Isothe.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/4VVF6T7F/ja034676g.html:text/html}, + groups = {trypsin} } @article{skillman_sampl3_2012, @@ -1934,7 +2021,8 @@ @article{skillman_sampl3_2012 year = {2012}, keywords = {overview,SAMPL,SAMPL3,trypsin}, pages = {473--474}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZXEXV4TQ/Skillman - 2012 - SAMPL3 blinded prediction of host–guest binding a.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZVXSPHDE/s10822-012-9580-z.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZXEXV4TQ/Skillman - 2012 - SAMPL3 blinded prediction of host–guest binding a.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZVXSPHDE/s10822-012-9580-z.html:text/html}, + groups = {trypsin} } @article{Newman:2011:JComputAidedMolDes, @@ -1954,7 +2042,8 @@ @article{Newman:2011:JComputAidedMolDes year = {2011}, keywords = {crystallography,experiment,SAMPL,SAMPL3,trypsin}, pages = {497--503}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DI58Q3BZ/Newman et al. - 2011 - The DINGO dataset a comprehensive set of data for.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DSAP4RSI/s10822-011-9521-2.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DI58Q3BZ/Newman et al. - 2011 - The DINGO dataset a comprehensive set of data for.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DSAP4RSI/s10822-011-9521-2.html:text/html}, + groups = {trypsin} } @article{de_ruiter_efficient_2012, @@ -1971,7 +2060,8 @@ @article{de_ruiter_efficient_2012 month = oct, year = {2012}, pages = {3686--3695}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/4S57876P/de Ruiter and Oostenbrink - 2012 - Efficient and Accurate Free Energy Calculations on.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AVZXQKWA/ct200750p.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/4S57876P/de Ruiter and Oostenbrink - 2012 - Efficient and Accurate Free Energy Calculations on.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AVZXQKWA/ct200750p.html:text/html}, + groups = {trypsin} } @article{jiao_calculation_2008, @@ -1991,6 +2081,7 @@ @article{jiao_calculation_2008 keywords = {benzamidine,force field,Molecular dynamics,simulation,trypsin}, pages = {6290--6295}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FQMHKZ2G/Jiao et al. - 2008 - Calculation of protein–ligand binding free energy .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FZN442NU/6290.html:text/html}, + groups = {trypsin}, pmid = {18427113} } @@ -2009,7 +2100,8 @@ @article{villa_sampling_2003 author = {Villa, Alessandra and Zangi, Ronen and Pieffet, Gilles and Mark, Alan E.}, year = {2003}, pages = {673--686}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I33JVJ9H/Villa et al. - Sampling and convergence in free energy calculatio.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/C3425PKX/BJCAM.0000017374.53591.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I33JVJ9H/Villa et al. - Sampling and convergence in free energy calculatio.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/C3425PKX/BJCAM.0000017374.53591.html:text/html}, + groups = {trypsin} } @article{jiao_trypsin_2009, @@ -2028,7 +2120,8 @@ @article{jiao_trypsin_2009 year = {2009}, keywords = {binding,force field,Free energy,polarizable,simulation,trypsin}, pages = {1701--1711}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BH3XHSP5/Jiao et al. - 2009 - Trypsin-ligand binding free energies from explicit.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HB6CAMVF/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BH3XHSP5/Jiao et al. - 2009 - Trypsin-ligand binding free energies from explicit.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HB6CAMVF/abstract.html:text/html}, + groups = {trypsin} } @article{gallicchio_virtual_2014, @@ -2048,7 +2141,8 @@ @article{gallicchio_virtual_2014 year = {2014}, keywords = {alchemical,HIV integrase,SAMPL,SAMPL4}, pages = {475--490}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/E8RDGITW/Gallicchio et al. - 2014 - Virtual screening of integrase inhibitors by large.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2W2FXFN7/10.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/E8RDGITW/Gallicchio et al. - 2014 - Virtual screening of integrase inhibitors by large.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2W2FXFN7/10.html:text/html}, + groups = {HIV integrase} } @article{mobley_blind_2014, @@ -2066,7 +2160,8 @@ @article{mobley_blind_2014 month = mar, year = {2014}, pages = {327--345}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/9NEJF2MW/Mobley et al. - 2014 - Blind prediction of HIV integrase binding from the.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/9G8PB6V4/s10822-014-9723-5.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/9NEJF2MW/Mobley et al. - 2014 - Blind prediction of HIV integrase binding from the.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/9G8PB6V4/s10822-014-9723-5.html:text/html}, + groups = {HIV integrase} } @article{peat_interrogating_2014, @@ -2084,7 +2179,8 @@ @article{peat_interrogating_2014 month = feb, year = {2014}, pages = {347--362}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/M78PCTBB/Peat et al. - 2014 - Interrogating HIV integrase for compounds that bin.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WEPFHXFG/10.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/M78PCTBB/Peat et al. - 2014 - Interrogating HIV integrase for compounds that bin.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WEPFHXFG/10.html:text/html}, + groups = {HIV integrase} } @article{jayachandran_parallelized-over-parts_2006, @@ -2102,7 +2198,8 @@ @article{jayachandran_parallelized-over-parts_2006 year = {2006}, keywords = {Conformational dynamics,Free energy,Molecular conformation,Proteins,Solvents}, pages = {084901}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/K92VJ5MM/Jayachandran et al. - 2006 - Parallelized-over-parts computation of absolute bi.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/47X68KBZ/1.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/K92VJ5MM/Jayachandran et al. - 2006 - Parallelized-over-parts computation of absolute bi.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/47X68KBZ/1.html:text/html}, + groups = {FKBP} } @article{ytreberg_absolute_2009, @@ -2120,7 +2217,8 @@ @article{ytreberg_absolute_2009 year = {2009}, keywords = {Computer software,Free energy,Jacobians,Jarzynski,nonequilibrium,PMF,Protein ligand interactions,Proteins}, pages = {164906}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/H72XPC9F/Ytreberg - 2009 - Absolute FKBP binding affinities obtained via none.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/TMJ3JT7H/1.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/H72XPC9F/Ytreberg - 2009 - Absolute FKBP binding affinities obtained via none.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/TMJ3JT7H/1.html:text/html}, + groups = {FKBP} } @article{fujitani_direct_2005, @@ -2138,7 +2236,8 @@ @article{fujitani_direct_2005 year = {2005}, keywords = {Amber,Computer simulation,Crystal structure,Free energy,Proteins}, pages = {084108}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2X5FG6AS/Fujitani et al. - 2005 - Direct calculation of the binding free energies of.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HH5MSXBE/1.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2X5FG6AS/Fujitani et al. - 2005 - Direct calculation of the binding free energies of.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HH5MSXBE/1.html:text/html}, + groups = {FKBP} } @article{fujitani_massively_2009, @@ -2154,7 +2253,8 @@ @article{fujitani_massively_2009 month = feb, year = {2009}, pages = {021914}, - file = {PhysRevE.79.021914.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/A873JXVA/PhysRevE.79.021914.pdf:application/pdf;APS Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/64TVJEQK/PhysRevE.79.html:text/html} + file = {PhysRevE.79.021914.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/A873JXVA/PhysRevE.79.021914.pdf:application/pdf;APS Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/64TVJEQK/PhysRevE.79.html:text/html}, + groups = {FKBP} } @article{wang_absolute_2006, @@ -2171,7 +2271,8 @@ @article{wang_absolute_2006 month = oct, year = {2006}, pages = {2798--2814}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/J85B3WPV/Wang et al. - 2006 - Absolute Binding Free Energy Calculations Using Mo.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SIZTA2BA/S0006349506719944.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/J85B3WPV/Wang et al. - 2006 - Absolute Binding Free Energy Calculations Using Mo.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/SIZTA2BA/S0006349506719944.html:text/html}, + groups = {FKBP} } @article{lee_calculation_2006, @@ -2189,7 +2290,8 @@ @article{lee_calculation_2006 year = {2006}, keywords = {alchemical,binding free energy,FKBP,PMF}, pages = {864--877}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DU46V42M/Lee and Olson - 2006 - Calculation of Absolute Protein-Ligand Binding Aff.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/6V43D6PV/S0006349506722743.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DU46V42M/Lee and Olson - 2006 - Calculation of Absolute Protein-Ligand Binding Aff.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/6V43D6PV/S0006349506722743.html:text/html}, + groups = {FKBP} } @book{shirts_calculating_2004, @@ -2199,7 +2301,8 @@ @book{shirts_calculating_2004 publisher = {{Stanford University}}, author = {Shirts, Michael R.}, year = {2004}, - file = {Calculating_precise_and_accurate_free_energies_in_.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WATUITI7/Calculating_precise_and_accurate_free_energies_in_.pdf:application/pdf} + file = {Calculating_precise_and_accurate_free_energies_in_.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WATUITI7/Calculating_precise_and_accurate_free_energies_in_.pdf:application/pdf}, + groups = {FKBP} } @article{smith_dihydropyrancarboxamides_1998, @@ -2218,7 +2321,8 @@ @article{smith_dihydropyrancarboxamides_1998 year = {1998}, keywords = {experiment,neuraminidase}, pages = {787--797}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZHU3ECDM/Smith et al. - 1998 - Dihydropyrancarboxamides Related to Zanamivir A .pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I88IGWDF/jm970374b.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZHU3ECDM/Smith et al. - 1998 - Dihydropyrancarboxamides Related to Zanamivir A .pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I88IGWDF/jm970374b.html:text/html}, + groups = {others} } @article{michel_protein_2006, @@ -2237,7 +2341,8 @@ @article{michel_protein_2006 year = {2006}, keywords = {alchemical,binding free energy,neuraminidase}, pages = {7427--7439}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/R5ANB8HV/Michel et al. - 2006 - Protein-Ligand Binding Affinity Predictions by Imp.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZD3MX3TI/jm061021s.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/R5ANB8HV/Michel et al. - 2006 - Protein-Ligand Binding Affinity Predictions by Imp.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ZD3MX3TI/jm061021s.html:text/html}, + groups = {others} } @article{kerry_structural_2013, @@ -2254,6 +2359,7 @@ @article{kerry_structural_2013 year = {2013}, keywords = {neuraminidase}, file = {PubMed Central Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/C792D28Q/Kerry et al. - 2013 - Structural basis for a class of nanomolar influenz.pdf:application/pdf}, + groups = {others}, pmid = {24129600}, pmcid = {PMC3797432} } @@ -2274,7 +2380,8 @@ @article{maurer_calculation_2016 year = {2016}, keywords = {computational alchemy,free-energy calculations,free-energy perturbation,GROMOS,molecular dynamics simulations,OppA,thermodynamic integration}, pages = {499}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AMS4AEU3/Maurer et al. - 2016 - Calculation of Relative Binding Free Energy in the.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/79MS8DZ3/htm.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AMS4AEU3/Maurer et al. - 2016 - Calculation of Relative Binding Free Energy in the.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/79MS8DZ3/htm.html:text/html}, + groups = {others} } @article{tame_crystal_1995, @@ -2284,7 +2391,7 @@ @article{tame_crystal_1995 doi = {10.1016/S0969-2126(01)00276-3}, abstract = {Background: The periplasmic oligopeptide-binding protein OppA has a remarkably broad substrate specificity, binding peptides of two to five amino-acid residues with high affinity, but little regard to sequence. It is therefore an ideal system for studying how different chemical groups can be accommodated in a protein interior. The ability of the protein to bind peptides of different lengths has been studied by co-crystallising it with different ligands. -Results Crystals of OppA from Salmonella typhimurium complexed with the peptides Lys\textendash{}Lys\textendash{}Lys (KKK) and Lys\textendash{}Lys\textendash{}Lys\textendash{}Ala (KKKA) have been grown in the presence of uranyl ions which form important crystal contacts. These structures have been refined to 1.4 \aa{} and 2.1 \aa, respectively. The ligands are completely enclosed, their side chains pointing into large hydrated cavities and making few strong interactions with the protein. +Results Crystals of OppA from Salmonella typhimurium complexed with the peptides Lys\textendash{}Lys\textendash{}Lys (KKK) and Lys\textendash{}Lys\textendash{}Lys\textendash{}Ala (KKKA) have been grown in the presence of uranyl ions which form important crystal contacts. These structures have been refined to 1.4 {\aa} and 2.1 {\aa}, respectively. The ligands are completely enclosed, their side chains pointing into large hydrated cavities and making few strong interactions with the protein. Conclusion Tight peptide binding by OppA arises from strong hydrogen bonding and electrostatic interactions between the protein and the main chain of the ligand. Different basic side chains on the protein form salt bridges with the C terminus of peptide ligands of different lengths.}, timestamp = {2016-09-01T18:44:30Z}, @@ -2296,7 +2403,8 @@ @article{tame_crystal_1995 year = {1995}, keywords = {oligopeptide,periplasmic binding protein,transport}, pages = {1395--1406}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QWU7CQCK/Tame et al. - 1995 - The crystal structures of the oligopeptide-binding.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I3ZC3SZH/S0969212601002763.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QWU7CQCK/Tame et al. - 1995 - The crystal structures of the oligopeptide-binding.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I3ZC3SZH/S0969212601002763.html:text/html}, + groups = {others} } @article{davies_relating_1999, @@ -2316,7 +2424,8 @@ @article{davies_relating_1999 year = {1999}, keywords = {calorimetry,crystallography,drug design,ligand binding,peptides}, pages = {1432--1444}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V8JFAW3I/Davies et al. - 1999 - Relating structure to thermodynamics The crystal .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/75GQGNXP/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V8JFAW3I/Davies et al. - 1999 - Relating structure to thermodynamics The crystal .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/75GQGNXP/abstract.html:text/html}, + groups = {others} } @article{sleigh_crystallographic_1999, @@ -2334,7 +2443,8 @@ @article{sleigh_crystallographic_1999 year = {1999}, keywords = {calorimetry,peptide-binding protein,water,X-ray crystallography}, pages = {393--415}, - file = {ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/66U8KGJT/S0022283699929297.html:text/html} + file = {ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/66U8KGJT/S0022283699929297.html:text/html}, + groups = {others} } @article{kaus_how_2015, @@ -2351,7 +2461,8 @@ @article{kaus_how_2015 month = jun, year = {2015}, pages = {2670--2679}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CHBJFX8P/Kaus et al. - 2015 - How To Deal with Multiple Binding Poses in Alchemi.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/KPHNAUX6/acs.jctc.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CHBJFX8P/Kaus et al. - 2015 - How To Deal with Multiple Binding Poses in Alchemi.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/KPHNAUX6/acs.jctc.html:text/html}, + groups = {others} } @article{freeman_cucurbituril_1981, @@ -2367,7 +2478,8 @@ @article{freeman_cucurbituril_1981 month = dec, year = {1981}, pages = {7367--7368}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3HS5CPSC/Freeman et al. - 1981 - Cucurbituril.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V7USZKV9/ja00414a070.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3HS5CPSC/Freeman et al. - 1981 - Cucurbituril.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V7USZKV9/ja00414a070.html:text/html}, + groups = {CB7} } @article{velez-vega_force_2012, @@ -2384,7 +2496,8 @@ @article{velez-vega_force_2012 month = mar, year = {2012}, pages = {966--976}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3ZRXIUKA/Velez-Vega and Gilson - 2012 - Force and Stress along Simulated Dissociation Path.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/C9W4UR33/ct2006902.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3ZRXIUKA/Velez-Vega and Gilson - 2012 - Force and Stress along Simulated Dissociation Path.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/C9W4UR33/ct2006902.html:text/html}, + groups = {CB7} } @article{velez-vega_overcoming_2013, @@ -2403,7 +2516,8 @@ @article{velez-vega_overcoming_2013 year = {2013}, keywords = {binding free energy,cucurbituril,ligand,molecular mechanics,statistical mechanics,steered molecular dynamics,umbrella sampling}, pages = {2360--2371}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/56R7DETA/Velez-Vega and Gilson - 2013 - Overcoming dissipation in the calculation of stand.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WECWTT5S/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/56R7DETA/Velez-Vega and Gilson - 2013 - Overcoming dissipation in the calculation of stand.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WECWTT5S/abstract.html:text/html}, + groups = {CB7} } @article{gilson_statistical-thermodynamic_1997, @@ -2516,7 +2630,7 @@ @article{armacost_biasing_2015 volume = {11}, issn = {1549-9618}, doi = {10.1021/ct500894k}, - abstract = {Traditional free energy calculation methods are well-known for their drawbacks in scalability and speed in converging results particularly for calculations with large perturbations. In the present work, we report on the development of biasing potential replica exchange multisite $\lambda$-dynamics (BP-REX MS$\lambda$D), which is a free energy method that is capable of performing simultaneous alchemical free energy transformations, including perturbations between flexible moieties. BP-REX MS$\lambda$D and the original MS$\lambda$D are applied to a series of symmetrical 2,5-benzoquinone derivatives covering a diverse chemical space and range of conformational flexibility. Improved $\lambda$-space sampling is observed for the BP-REX MS$\lambda$D simulations, yielding a 2\textendash{}5-fold increase in the number of transitions between substituents compared to traditional MS$\lambda$D. We also demonstrate the efficacy of varying the value of c, the parameter that controls the ruggedness of the landscape mediating the sampling of $\lambda$-states, based on the flexibility of the fragment. Finally, we developed a protocol for maximizing the transition frequency between fragments. This protocol reduces the ``kinetic barrier'' for alchemically transforming fragments by grouping and ordering based on volume. These findings are applied to a challenging test set involving a series of geldanamycin-based inhibitors of heat shock protein 90 (Hsp90). Even though the perturbations span volume changes by as large as 60 \AA{}3, the values for the free energy change achieve an average unsigned error (AUE) of 1.5 kcal/mol relative to experimental Kd measurements with a reasonable correlation (R = 0.56). Our results suggest that the BP-REX MS$\lambda$D algorithm is a highly efficient and scalable free energy method, which when utilized will enable routine calculations on the order of hundreds of compounds using only a few simulations.}, + abstract = {Traditional free energy calculation methods are well-known for their drawbacks in scalability and speed in converging results particularly for calculations with large perturbations. In the present work, we report on the development of biasing potential replica exchange multisite $\lambda$-dynamics (BP-REX MS$\lambda$D), which is a free energy method that is capable of performing simultaneous alchemical free energy transformations, including perturbations between flexible moieties. BP-REX MS$\lambda$D and the original MS$\lambda$D are applied to a series of symmetrical 2,5-benzoquinone derivatives covering a diverse chemical space and range of conformational flexibility. Improved $\lambda$-space sampling is observed for the BP-REX MS$\lambda$D simulations, yielding a 2\textendash{}5-fold increase in the number of transitions between substituents compared to traditional MS$\lambda$D. We also demonstrate the efficacy of varying the value of c, the parameter that controls the ruggedness of the landscape mediating the sampling of $\lambda$-states, based on the flexibility of the fragment. Finally, we developed a protocol for maximizing the transition frequency between fragments. This protocol reduces the ``kinetic barrier'' for alchemically transforming fragments by grouping and ordering based on volume. These findings are applied to a challenging test set involving a series of geldanamycin-based inhibitors of heat shock protein 90 (Hsp90). Even though the perturbations span volume changes by as large as 60 {\AA}3, the values for the free energy change achieve an average unsigned error (AUE) of 1.5 kcal/mol relative to experimental Kd measurements with a reasonable correlation (R = 0.56). Our results suggest that the BP-REX MS$\lambda$D algorithm is a highly efficient and scalable free energy method, which when utilized will enable routine calculations on the order of hundreds of compounds using only a few simulations.}, timestamp = {2016-09-02T17:50:49Z}, number = {3}, urldate = {2016-09-02}, @@ -2641,7 +2755,8 @@ @article{calabro_accelerating_2015 author = {Calabr{\`o}, Gaetano}, month = nov, year = {2015}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/8SZ5WZKM/Calabrò - 2015 - Accelerating molecular simulations implication for.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/65WKVZDN/16439.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/8SZ5WZKM/Calabrò - 2015 - Accelerating molecular simulations implication for.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/65WKVZDN/16439.html:text/html}, + groups = {thrombin} } @article{eriksson_cavity-containing_1992, @@ -2659,7 +2774,8 @@ @article{eriksson_cavity-containing_1992 month = jan, year = {1992}, pages = {371--373}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/VVWJD72T/Eriksson et al. - 1992 - A cavity-containing mutant of T4 lysozyme is stabi.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/6ANUMM4C/355371a0.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/VVWJD72T/Eriksson et al. - 1992 - A cavity-containing mutant of T4 lysozyme is stabi.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/6ANUMM4C/355371a0.html:text/html}, + groups = {lysozyme} } @book{allen_computer_1989, @@ -2704,7 +2820,7 @@ @article{jorgensen_efficient_1988 volume = {89}, issn = {0021-9606, 1089-7690}, doi = {10.1063/1.454895}, - abstract = {An efficient procedure is noted for computing absolute free energies of binding for complexes in solution. Two series of computer simulations are required in which the substrate is annihilated in the solvent by itself and in the solvated complex. For illustration, the free energy of binding for two methane-like particles at their contact separation of 4 \AA{} has been computed in TIP4P water. Though several alternatives are possible, in this case, Monte Carlo simulations were employed with statistical perturbation theory in the NPT ensemble at 25 $^\circ$C and 1 atm. The results for the free energy of binding as well as for the potential of mean force are consistent with prior findings from the integral equation theory of Pratt and Chandler.}, + abstract = {An efficient procedure is noted for computing absolute free energies of binding for complexes in solution. Two series of computer simulations are required in which the substrate is annihilated in the solvent by itself and in the solvated complex. For illustration, the free energy of binding for two methane-like particles at their contact separation of 4 {\AA} has been computed in TIP4P water. Though several alternatives are possible, in this case, Monte Carlo simulations were employed with statistical perturbation theory in the NPT ensemble at 25 $^\circ$C and 1 atm. The results for the free energy of binding as well as for the potential of mean force are consistent with prior findings from the integral equation theory of Pratt and Chandler.}, timestamp = {2016-09-07T17:46:10Z}, number = {6}, urldate = {2016-09-07}, @@ -2796,11 +2912,12 @@ @article{Gibb:2004:J.Am.Chem.Soc. month = sep, year = {2004}, pages = {11408--11409}, + groups = {MKG}, pmid = {15366865} } @article{Cong:2016:Org.Biomol.Chem., - title = {Synthesis and Separation of Cucurbit[n]urils and Their Derivatives}, + title = {Synthesis and Separation of Cucurbit[n]Urils and Their Derivatives}, volume = {14}, issn = {1477-0539}, doi = {10.1039/c6ob00268d}, @@ -2813,11 +2930,12 @@ @article{Cong:2016:Org.Biomol.Chem. month = may, year = {2016}, pages = {4335--4364}, + groups = {CB7,MKG}, pmid = {26991738} } @article{vinciguerra_synthesis_2015, - title = {Synthesis and {{Recognition Properties}} of {{Cucurbit}}[8]uril {{Derivatives}}}, + title = {Synthesis and {{Recognition Properties}} of {{Cucurbit}}[8]Uril {{Derivatives}}}, volume = {17}, issn = {1523-7052}, doi = {10.1021/acs.orglett.5b02558}, @@ -2830,6 +2948,7 @@ @article{vinciguerra_synthesis_2015 month = oct, year = {2015}, pages = {5068--5071}, + groups = {CB7,MKG}, pmid = {26405845} } @@ -2848,6 +2967,7 @@ @article{assaf_cucurbiturils:_2015 month = jan, year = {2015}, pages = {394--418}, + groups = {CB7,MKG}, pmid = {25317670} } @@ -2864,7 +2984,8 @@ @article{jorgensen_quantum_1981 author = {Jorgensen, William L.}, month = jan, year = {1981}, - pages = {345--350} + pages = {345--350}, + groups = {MKG} } @article{Lee:2003:Acc.Chem.Res., @@ -2882,6 +3003,7 @@ @article{Lee:2003:Acc.Chem.Res. month = aug, year = {2003}, pages = {621--630}, + groups = {CB7}, pmid = {12924959} } @@ -2899,7 +3021,8 @@ @article{dunbar_csar_2011 author = {Dunbar, James B. and Smith, Richard D. and Yang, Chao-Yie and Ung, Peter Man-Un and Lexa, Katrina W. and Khazanov, Nickolay A. and Stuckey, Jeanne A. and Wang, Shaomeng and Carlson, Heather A.}, month = sep, year = {2011}, - pages = {2036--2046} + pages = {2036--2046}, + groups = {MKG} } @article{flyvbjerg_error_1989, @@ -2915,7 +3038,8 @@ @article{flyvbjerg_error_1989 author = {Flyvbjerg, H. and Petersen, H. G.}, month = jul, year = {1989}, - pages = {461} + pages = {461}, + groups = {MKG} } @article{tai_conformational_2004, @@ -2932,7 +3056,8 @@ @article{tai_conformational_2004 month = feb, year = {2004}, pages = {213--220}, - file = {1-s2.0-S0301462203002813-main.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NGJEE54M/1-s2.0-S0301462203002813-main.pdf:application/pdf} + file = {1-s2.0-S0301462203002813-main.pdf:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NGJEE54M/1-s2.0-S0301462203002813-main.pdf:application/pdf}, + groups = {MKG} } @article{Lee:2003:AccountsofChemicalResearch, @@ -2947,7 +3072,8 @@ @article{Lee:2003:AccountsofChemicalResearch journal = {Accounts of Chemical Research}, author = {Lee, Jae Wook and Samal, S. and Selvapalam, N. and Kim, Hee-Joon and Kim, Kimoon}, year = {2003}, - pages = {621--630} + pages = {621--630}, + groups = {MKG} } @article{shirts_lessons_2016, @@ -2974,6 +3100,7 @@ @article{eklund_cluster_2016 year = {2016}, keywords = {cluster inference,false positives,fMRI,permutation test,statistics}, pages = {7900--7905}, + groups = {MKG}, pmid = {27357684}, pmcid = {PMC4948312} } @@ -2990,6 +3117,7 @@ @article{rekharsky_complexation_1998 month = jul, year = {1998}, pages = {1875--1918}, + groups = {cyclodextrin,MKG}, pmid = {11848952} } @@ -3017,12 +3145,12 @@ @article{yin_overview_2016 doi = {10.1007/s10822-016-9974-4}, abstract = {The ability to computationally predict protein-small molecule binding affinities with high accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial-and-error synthesis and experimental evaluation of candidate ligands. As academic and industrial groups work toward this capability, there is an ongoing need for datasets that can be used to rigorously test new computational methods. Although protein\textendash{}ligand data are clearly important for this purpose, their size and complexity make it difficult to obtain well-converged results and to troubleshoot computational methods. Host\textendash{}guest systems offer a valuable alternative class of test cases, as they exemplify noncovalent molecular recognition but are far smaller and simpler. As a consequence, host\textendash{}guest systems have been part of the prior two rounds of SAMPL prediction exercises, and they also figure in the present SAMPL5 round. In addition to being blinded, and thus avoiding biases that may arise in retrospective studies, the SAMPL challenges have the merit of focusing multiple researchers on a common set of molecular systems, so that methods may be compared and ideas exchanged. The present paper provides an overview of the host\textendash{}guest component of SAMPL5, which centers on three different hosts, two octa-acids and a glycoluril-based molecular clip, and two different sets of guest molecules, in aqueous solution. A range of methods were applied, including electronic structure calculations with implicit solvent models; methods that combine empirical force fields with implicit solvent models; and explicit solvent free energy simulations. The most reliable methods tend to fall in the latter class, consistent with results in prior SAMPL rounds, but the level of accuracy is still below that sought for reliable computer-aided drug design. Advances in force field accuracy, modeling of protonation equilibria, electronic structure methods, and solvent models, hold promise for future improvements.}, language = {en}, - timestamp = {2016-09-22T21:04:27Z}, + timestamp = {2017-03-01T18:19:14Z}, + number = {31}, urldate = {2016-09-22}, journal = {J Comput Aided Mol Des}, author = {Yin, Jian and Henriksen, Niel M. and Slochower, David R. and Shirts, Michael R. and Chiu, Michael W. and Mobley, David L. and Gilson, Michael K.}, - month = sep, - year = {2016}, + year = {2017}, keywords = {CBClip,host–guest complexation,OctaAcid,overview,SAMPL,SAMPL5}, pages = {1--19}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/22989I64/Yin et al. - 2016 - Overview of the SAMPL5 host–guest challenge Are w.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5NTTWBRW/s10822-016-9974-4.html:text/html} @@ -3099,7 +3227,7 @@ @article{Marquez:2004:J.Am.Chem.Soc. volume = {126}, issn = {0002-7863}, doi = {10.1021/ja0319846}, - abstract = {The factors affecting host-guest complexation between the molecular container compound cucurbit[6]uril (CB6) and various guests in aqueous solution are studied, and a detailed complexation mechanism in the presence of cations is derived. The formation of the supramolecular complex is studied in detail for cyclohexylmethylammonium ion as guest. The kinetics and thermodynamics of complexation is monitored by NMR as a function of temperature, salt concentration, and cation size. The binding constants and the ingression rate constants decrease with increasing salt concentration and cation-binding constant, in agreement with a competitive binding of the ammonium site of the guest and the metal cation with the ureido carbonyl portals of CB6. Studies as a function of guest size indicate that the effective container volume of the CB6 cavity is approximately 105 \AA{}3. It is suggested that larger guests are excluded for two reasons:\, a high activation barrier for ingression imposed by the tight CB6 portals and a destabilization of the complex due to steric repulsion inside. For example, in the case of the nearly spherical azoalkane homologues 2,3-diazabicyclo[2.2.1]hept-2-ene (DBH, volume ca. 96 \AA{}3) and 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO, volume ca. 110 \AA{}3), the former forms the CB6 complex promptly with a sizable binding constant (1300 M-1), while the latter does not form a complex even after several months at optimized complexation conditions. Molecular mechanics calculations are performed for several CB6/guest complexes. A qualitative agreement is found between experimental and calculated activation energies for ingression as a function of both guest size and state of protonation. The potential role of constrictive binding by CB6 is discussed.}, + abstract = {The factors affecting host-guest complexation between the molecular container compound cucurbit[6]uril (CB6) and various guests in aqueous solution are studied, and a detailed complexation mechanism in the presence of cations is derived. The formation of the supramolecular complex is studied in detail for cyclohexylmethylammonium ion as guest. The kinetics and thermodynamics of complexation is monitored by NMR as a function of temperature, salt concentration, and cation size. The binding constants and the ingression rate constants decrease with increasing salt concentration and cation-binding constant, in agreement with a competitive binding of the ammonium site of the guest and the metal cation with the ureido carbonyl portals of CB6. Studies as a function of guest size indicate that the effective container volume of the CB6 cavity is approximately 105 {\AA}3. It is suggested that larger guests are excluded for two reasons:\, a high activation barrier for ingression imposed by the tight CB6 portals and a destabilization of the complex due to steric repulsion inside. For example, in the case of the nearly spherical azoalkane homologues 2,3-diazabicyclo[2.2.1]hept-2-ene (DBH, volume ca. 96 {\AA}3) and 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO, volume ca. 110 {\AA}3), the former forms the CB6 complex promptly with a sizable binding constant (1300 M-1), while the latter does not form a complex even after several months at optimized complexation conditions. Molecular mechanics calculations are performed for several CB6/guest complexes. A qualitative agreement is found between experimental and calculated activation energies for ingression as a function of both guest size and state of protonation. The potential role of constrictive binding by CB6 is discussed.}, timestamp = {2016-12-06T22:40:06Z}, number = {18}, urldate = {2016-12-06}, @@ -3108,7 +3236,8 @@ @article{Marquez:2004:J.Am.Chem.Soc. month = may, year = {2004}, pages = {5806--5816}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ERRPBQ7D/Márquez et al. - 2004 - Mechanism of Host−Guest Complexation by Cucurbitur.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RHMAE6CS/ja0319846.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ERRPBQ7D/Márquez et al. - 2004 - Mechanism of Host−Guest Complexation by Cucurbitur.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RHMAE6CS/ja0319846.html:text/html}, + groups = {CB7} } @article{Fitzgerald:1995:ProteinScience, @@ -3127,7 +3256,8 @@ @article{Fitzgerald:1995:ProteinScience year = {1995}, keywords = {cytochrome c peroxidase,engineered binding site,enzyme-substrate binding,protein cavities,Protein engineering,tryptophan radical cation,X-ray crystallography}, pages = {1844--1850}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3PME9DKM/Fitzgerald et al. - 1995 - The role of aspartate-235 in the binding of cation.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AI9B64S9/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3PME9DKM/Fitzgerald et al. - 1995 - The role of aspartate-235 in the binding of cation.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AI9B64S9/abstract.html:text/html}, + groups = {CCP} } @article{Bento:2014:NuclAcidsRes, @@ -3180,7 +3310,8 @@ @article{StefanicAnderluh:2005:J.Med.Chem. month = may, year = {2005}, pages = {3110--3113}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/S6BUP62K/Štefanič Anderluh et al. - 2005 - Toward a Novel Class of Antithrombotic Compounds w.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7JQ327CK/jm048984g.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/S6BUP62K/Štefanič Anderluh et al. - 2005 - Toward a Novel Class of Antithrombotic Compounds w.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7JQ327CK/jm048984g.html:text/html}, + groups = {thrombin} } @article{Ueno:2005:Bioorganic&MedicinalChemistryLetters, @@ -3198,7 +3329,8 @@ @article{Ueno:2005:Bioorganic&MedicinalChemistryLetters year = {2005}, keywords = {Antithrombotic effect on venous thrombosis in rats,Inhibition of human FXa,JTV-803,Potent and selective factor Xa (FXa) inhibitor,Tetrahydroisoquinoline derivatives}, pages = {185--189}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/9AXWI3GN/Ueno et al. - 2005 - Discovery of novel tetrahydroisoquinoline derivati.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/8KI7KDDG/S0960894X04012612.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/9AXWI3GN/Ueno et al. - 2005 - Discovery of novel tetrahydroisoquinoline derivati.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/8KI7KDDG/S0960894X04012612.html:text/html}, + groups = {thrombin} } @article{Putta:2005:J.Med.Chem., @@ -3216,11 +3348,12 @@ @article{Putta:2005:J.Med.Chem. month = may, year = {2005}, pages = {3313--3318}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/E62XJRMF/Putta et al. - 2005 - Conformation Mining An Algorithm for Finding Bio.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/KT8M2CT5/jm049066l.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/E62XJRMF/Putta et al. - 2005 - Conformation Mining An Algorithm for Finding Bio.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/KT8M2CT5/jm049066l.html:text/html}, + groups = {thrombin} } @article{Dullweber:2001:JournalofMolecularBiology, - title = {Factorising Ligand Affinity: A Combined Thermodynamic and Crystallographic Study of Trypsin and Thrombin inhibition\textdagger\textdagger{}2}, + title = {Factorising Ligand Affinity: A Combined Thermodynamic and Crystallographic Study of Trypsin and Thrombin Inhibition\textdagger\textdagger{}2}, volume = {313}, issn = {0022-2836}, shorttitle = {Factorising Ligand Affinity}, @@ -3230,12 +3363,13 @@ @article{Dullweber:2001:JournalofMolecularBiology number = {3}, urldate = {2016-12-07}, journal = {Journal of Molecular Biology}, - author = {Dullweber, Frank and Stubbs, Milton T and Musil, \DJ{}or\dj{}e and St{\"u}rzebecher, J{\"o}rg and Klebe, Gerhard}, + author = {Dullweber, Frank and Stubbs, Milton T and Musil, {\DJ}or{\dj}e and St{\"u}rzebecher, J{\"o}rg and Klebe, Gerhard}, month = oct, year = {2001}, keywords = {drug design,enthalpy-entropy compensation,isothermal titration calorimetry,Thermodynamics,X-ray crystallography}, pages = {593--614}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/P5T8DHJC/Dullweber et al. - 2001 - Factorising ligand affinity a combined thermodyna.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/K9JNP53T/S0022283601950624.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/P5T8DHJC/Dullweber et al. - 2001 - Factorising ligand affinity a combined thermodyna.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/K9JNP53T/S0022283601950624.html:text/html}, + groups = {thrombin} } @article{Filippakopoulos:2010:Nature, @@ -3255,7 +3389,8 @@ @article{Filippakopoulos:2010:Nature year = {2010}, keywords = {Cancer,Drug discovery,Structural biology}, pages = {1067--1073}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MEWH4ECC/Filippakopoulos et al. - 2010 - Selective inhibition of BET bromodomains.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DC38J6EN/nature09504.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MEWH4ECC/Filippakopoulos et al. - 2010 - Selective inhibition of BET bromodomains.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DC38J6EN/nature09504.html:text/html}, + groups = {bromodomains} } @article{Chung:2011:J.Med.Chem., @@ -3272,7 +3407,8 @@ @article{Chung:2011:J.Med.Chem. month = jun, year = {2011}, pages = {3827--3838}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/XBIJVDS5/Chung et al. - 2011 - Discovery and Characterization of Small Molecule I.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WS78V7BX/jm200108t.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/XBIJVDS5/Chung et al. - 2011 - Discovery and Characterization of Small Molecule I.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WS78V7BX/jm200108t.html:text/html}, + groups = {bromodomains} } @article{Hewings:2012:J.Med.Chem., @@ -3289,7 +3425,8 @@ @article{Hewings:2012:J.Med.Chem. month = nov, year = {2012}, pages = {9393--9413}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/A48MQ565/Hewings et al. - 2012 - Progress in the Development and Application of Sma.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/8RXR4QQS/jm300915b.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/A48MQ565/Hewings et al. - 2012 - Progress in the Development and Application of Sma.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/8RXR4QQS/jm300915b.html:text/html}, + groups = {bromodomains} } @article{Bamborough:2015:J.Med.Chem., @@ -3306,7 +3443,8 @@ @article{Bamborough:2015:J.Med.Chem. month = aug, year = {2015}, pages = {6151--6178}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FDSGPG34/Bamborough et al. - 2015 - Structure-Based Optimization of Naphthyridones int.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/XDBZFXET/acs.jmedchem.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FDSGPG34/Bamborough et al. - 2015 - Structure-Based Optimization of Naphthyridones int.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/XDBZFXET/acs.jmedchem.html:text/html}, + groups = {bromodomains} } @article{Ran:2015:J.Med.Chem., @@ -3314,7 +3452,7 @@ @article{Ran:2015:J.Med.Chem. volume = {58}, issn = {0022-2623}, doi = {10.1021/acs.jmedchem.5b00613}, - abstract = {Small-molecule inhibitors of bromodomain and extra terminal proteins (BET), including BRD2, BRD3, and BRD4 proteins have therapeutic potential for the treatment of human cancers and other diseases and conditions. In this paper, we report the design, synthesis, and evaluation of $\gamma$-carboline-containing compounds as a new class of small-molecule BET inhibitors. The most potent inhibitor (compound 18, RX-37) obtained from this study binds to BET bromodomain proteins (BRD2, BRD3, and BRD4) with Ki values of 3.2\textendash{}24.7 nM and demonstrates high selectivity over other non-BET bromodomain-containing proteins. Compound 18 potently and selectively inhibits cell growth in human acute leukemia cell lines harboring the rearranged mixed lineage leukemia 1 gene. We have determined a cocrystal structure of 18 in complex with BRD4 BD2 at 1.4 \AA{} resolution, which provides a solid structural basis for the compound's high binding affinity and for its further structure-based optimization. Compound 18 represents a promising lead compound for the development of a new class of therapeutics for the treatment of human cancer and other conditions.}, + abstract = {Small-molecule inhibitors of bromodomain and extra terminal proteins (BET), including BRD2, BRD3, and BRD4 proteins have therapeutic potential for the treatment of human cancers and other diseases and conditions. In this paper, we report the design, synthesis, and evaluation of $\gamma$-carboline-containing compounds as a new class of small-molecule BET inhibitors. The most potent inhibitor (compound 18, RX-37) obtained from this study binds to BET bromodomain proteins (BRD2, BRD3, and BRD4) with Ki values of 3.2\textendash{}24.7 nM and demonstrates high selectivity over other non-BET bromodomain-containing proteins. Compound 18 potently and selectively inhibits cell growth in human acute leukemia cell lines harboring the rearranged mixed lineage leukemia 1 gene. We have determined a cocrystal structure of 18 in complex with BRD4 BD2 at 1.4 {\AA} resolution, which provides a solid structural basis for the compound's high binding affinity and for its further structure-based optimization. Compound 18 represents a promising lead compound for the development of a new class of therapeutics for the treatment of human cancer and other conditions.}, timestamp = {2016-12-07T00:28:37Z}, number = {12}, urldate = {2016-12-07}, @@ -3323,7 +3461,8 @@ @article{Ran:2015:J.Med.Chem. month = jun, year = {2015}, pages = {4927--4939}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BFKU5W5U/Ran et al. - 2015 - Structure-Based Design of γ-Carboline Analogues as.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RIFC3PVD/acs.jmedchem.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BFKU5W5U/Ran et al. - 2015 - Structure-Based Design of γ-Carboline Analogues as.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RIFC3PVD/acs.jmedchem.html:text/html}, + groups = {bromodomains} } @article{Zhang:2013:J.Med.Chem., @@ -3340,7 +3479,8 @@ @article{Zhang:2013:J.Med.Chem. month = nov, year = {2013}, pages = {9251--9264}, - 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author = {Luzhkov, Victor and \AA{}qvist, Johan}, + author = {Luzhkov, Victor and {\AA}qvist, Johan}, month = mar, year = {1999}, pages = {267--272}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DSMRSRHD/Luzhkov and Åqvist - 1999 - Free-energy perturbation calculations of binding a.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I24G6K6H/S0009261499001098.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DSMRSRHD/Luzhkov and Åqvist - 1999 - Free-energy perturbation calculations of binding a.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I24G6K6H/S0009261499001098.html:text/html}, + groups = {cyclodextrin} } @article{Bea:2002:TheorChemAcc, @@ -3624,7 +3778,8 @@ @article{Bea:2002:TheorChemAcc month = nov, year = {2002}, pages = {286--292}, - 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2008 - Molecular Dynamics Simulations of β-Cyclodextrin−A.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DDKANF2B/jp075493+.html:text/html}, + groups = {cyclodextrin} } @article{Cai:2009:J.Phys.Chem.B, @@ -3676,7 +3833,8 @@ @article{Cai:2009:J.Phys.Chem.B month = jun, year = {2009}, pages = {7836--7843}, - file = {ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NMM4PFK5/jp901825w.html:text/html} + file = {ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NMM4PFK5/jp901825w.html:text/html}, + groups = {cyclodextrin} } @article{ShengCai:2011:CurrentOrganicChemistry, @@ -3692,7 +3850,8 @@ @article{ShengCai:2011:CurrentOrganicChemistry year = {2011}, keywords = {complexation,cyclodextrins,free-energy calculations,Host-Guest Chemistry,molecular dynamics simulations}, pages = {839--847}, - file = {IngentaConnect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BK8V22JQ/Sheng Cai et al. - 2011 - Free Energy Calculations for Cyclodextrin Inclusio.pdf:application/pdf} + file = {IngentaConnect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BK8V22JQ/Sheng Cai et al. - 2011 - Free Energy Calculations for Cyclodextrin Inclusio.pdf:application/pdf}, + groups = {cyclodextrin} } @article{Wickstrom:2013:J.Chem.TheoryComput., @@ -3710,7 +3869,8 @@ @article{Wickstrom:2013:J.Chem.TheoryComput. month = jul, year = {2013}, pages = {3136--3150}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HV9CMMQR/Wickstrom et al. - 2013 - Large Scale Affinity Calculations of Cyclodextrin .pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7W3466H6/ct400003r.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/HV9CMMQR/Wickstrom et al. - 2013 - Large Scale Affinity Calculations of Cyclodextrin .pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7W3466H6/ct400003r.html:text/html}, + groups = {cyclodextrin} } @article{Shi:2014:TheorChemAcc, @@ -3729,7 +3889,8 @@ @article{Shi:2014:TheorChemAcc month = oct, year = {2014}, pages = {1556}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5HDB8JG6/Shi et al. - 2014 - Stereoselective inclusion mechanism of ketoprofen .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DVS5C3PB/s00214-014-1556-8.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/5HDB8JG6/Shi et al. - 2014 - Stereoselective inclusion mechanism of ketoprofen .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DVS5C3PB/s00214-014-1556-8.html:text/html}, + groups = {cyclodextrin} } @article{Zhang:2015:J.Chem.TheoryComput., @@ -3747,7 +3908,8 @@ @article{Zhang:2015:J.Chem.TheoryComput. month = nov, year = {2015}, pages = {5103--5113}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AEA78Q3T/Zhang et al. - 2015 - Generalized Born and Explicit Solvent Models for F.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WBXAKM36/acs.jctc.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AEA78Q3T/Zhang et al. - 2015 - Generalized Born and Explicit Solvent Models for F.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/WBXAKM36/acs.jctc.html:text/html}, + groups = {cyclodextrin} } @article{Khuntawee:2016:CarbohydratePolymers, @@ -3765,7 +3927,8 @@ @article{Khuntawee:2016:CarbohydratePolymers year = {2016}, keywords = {Conformational changes,ɛ-Cyclodextrin,Large-ring cyclodextrin,Replica exchange molecular dynamics}, pages = {99--105}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DH4662HX/Khuntawee et al. - 2016 - Conformation study of ɛ-cyclodextrin Replica exch.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ASMB8GNQ/S0144861715009984.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DH4662HX/Khuntawee et al. - 2016 - Conformation study of ɛ-cyclodextrin Replica exch.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/ASMB8GNQ/S0144861715009984.html:text/html}, + groups = {cyclodextrin} } @article{Gebhardt:2016:FluidPhaseEquilibria, @@ -3783,7 +3946,8 @@ @article{Gebhardt:2016:FluidPhaseEquilibria year = {2016}, keywords = {Cyclodextrin,force field,Free energy,Molecular dynamics}, pages = {1--17}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UVA9NBCA/Gebhardt and Hansen - 2016 - Calculation of binding affinities for linear alcoh.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2EV4F4WG/S0378381216300516.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UVA9NBCA/Gebhardt and Hansen - 2016 - Calculation of binding affinities for linear alcoh.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2EV4F4WG/S0378381216300516.html:text/html}, + groups = {cyclodextrin} } @article{Kirschner:2008:J.Comput.Chem., @@ -3803,7 +3967,8 @@ @article{Kirschner:2008:J.Comput.Chem. year = {2008}, keywords = {Amber,carbohydrate,force field,GLYCAM,Molecular dynamics,parameter development}, pages = {622--655}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/W4VHGZZV/Kirschner et al. - 2008 - GLYCAM06 A generalizable biomolecular force field.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/TZ35RZUU/abstract.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/W4VHGZZV/Kirschner et al. - 2008 - GLYCAM06 A generalizable biomolecular force field.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/TZ35RZUU/abstract.html:text/html}, + groups = {cyclodextrin} } @article{Cezard:2011:PhysicalChemistryChemicalPhysics, @@ -3819,7 +3984,8 @@ @article{Cezard:2011:PhysicalChemistryChemicalPhysics author = {C{\'e}zard, Christine and Trivelli, Xavier and Aubry, Fr{\'e}d{\'e}ric and Djeda{\"\i}ni-Pilard, Florence and Dupradeau, Fran{\c c}ois-Yves}, year = {2011}, pages = {15103--15121}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/KZQ9B7HH/Cézard et al. - 2011 - Molecular dynamics studies of native and substitut.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/B579VHJU/c1cp20854c.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/KZQ9B7HH/Cézard et al. - 2011 - Molecular dynamics studies of native and substitut.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/B579VHJU/c1cp20854c.html:text/html}, + groups = {cyclodextrin} } @article{Guvench:2011:J.Chem.TheoryComput., @@ -3836,7 +4002,8 @@ @article{Guvench:2011:J.Chem.TheoryComput. month = oct, year = {2011}, pages = {3162--3180}, - file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NP5X3XZX/Guvench et al. - 2011 - CHARMM Additive All-Atom Force Field for Carbohydr.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/B45MM42W/ct200328p.html:text/html} + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/NP5X3XZX/Guvench et al. - 2011 - CHARMM Additive All-Atom Force Field for Carbohydr.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/B45MM42W/ct200328p.html:text/html}, + groups = {cyclodextrin} } @article{Xiong:2015:CarbohydrateResearch, @@ -3853,7 +4020,8 @@ @article{Xiong:2015:CarbohydrateResearch year = {2015}, keywords = {Carbohydrate force field,Carbohydrate–protein interaction,drug design,Scoring function,simulation}, pages = {73--81}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3AFXIBBG/Xiong et al. - 2015 - Force fields and scoring functions for carbohydrat.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CES6PKWF/S0008621514004017.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3AFXIBBG/Xiong et al. - 2015 - Force fields and scoring functions for carbohydrat.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CES6PKWF/S0008621514004017.html:text/html}, + groups = {cyclodextrin} } @inproceedings{Mic:2013:AIPConferenceProceedings, @@ -3866,12 +4034,13 @@ @inproceedings{Mic:2013:AIPConferenceProceedings urldate = {2016-12-08}, booktitle = {{{AIP Conference Proceedings}}}, publisher = {{AIP Publishing}}, - author = {Mic, Mihaela and P\i\^rn{\u a}u, Adrian and Bogdan, Mircea and Turcu, Ioan}, + author = {Mic, Mihaela and P{\i}\^rn{\u a}u, Adrian and Bogdan, Mircea and Turcu, Ioan}, month = nov, year = {2013}, keywords = {Calorimeters,Data analysis,Differential scanning calorimeters,Equilibrium constants,Nuclear magnetic resonance}, pages = {63--66}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7PWVH9XH/Mic et al. - 2013 - Inclusion complex of benzocaine and β-cyclodextrin.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AKBMK5J2/1.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/7PWVH9XH/Mic et al. - 2013 - Inclusion complex of benzocaine and β-cyclodextrin.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/AKBMK5J2/1.html:text/html}, + groups = {cyclodextrin} } @book{Dodziuk:2006:, @@ -3879,7 +4048,8 @@ @book{Dodziuk:2006: timestamp = {2016-12-08T22:26:43Z}, publisher = {{John Wiley \& Sons}}, author = {Dodziuk, H}, - year = {2006} + year = {2006}, + groups = {cyclodextrin} } @incollection{Fromming:1994:CyclodextrinsinPharmacy, @@ -3888,7 +4058,8 @@ @incollection{Fromming:1994:CyclodextrinsinPharmacy booktitle = {Cyclodextrins in {{Pharmacy}}}, author = {Fr{\"o}mming, K.-H. and Szejtli, J{\'o}zsef}, year = {1994}, - pages = {19--32} + pages = {19--32}, + groups = {cyclodextrin} } @article{Gilson:2016:Nucl.AcidsRes., @@ -3928,11 +4099,12 @@ @article{Nucci:2014:PNAS keywords = {high-pressure NMR,protein folding and cooperativity,protein hydration,protein stability,reverse micelle encapsulation}, pages = {13846--13851}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/QXA5DR8H/Nucci et al. - 2014 - Role of cavities and hydration in the pressure unf.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MP3I9CDX/13846.html:text/html}, + groups = {lysozyme}, pmid = {25201963} } @article{Kitahara:2015:PNAS, - title = {Is Pressure-Induced Signal Loss in {{NMR}} Spectra for the {{Leu99Ala}} Cavity Mutant of {{T4}} Lysozyme due to Unfolding?}, + title = {Is Pressure-Induced Signal Loss in {{NMR}} Spectra for the {{Leu99Ala}} Cavity Mutant of {{T4}} Lysozyme Due to Unfolding?}, volume = {112}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.1423279112}, @@ -3947,6 +4119,7 @@ @article{Kitahara:2015:PNAS year = {2015}, pages = {E923--E923}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/V99CIRWQ/Kitahara and Mulder - 2015 - Is pressure-induced signal loss in NMR spectra for.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/R6EMJKZW/E923.html:text/html}, + groups = {lysozyme}, pmid = {25630507} } @@ -3967,6 +4140,7 @@ @article{Wand:2015:PNAS year = {2015}, pages = {E924--E924}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/2PS7GRTU/Wand and Nucci - 2015 - Reply to Kitahara and Mulder An ensemble view of .pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/I4W58GNF/E924.html:text/html}, + groups = {lysozyme}, pmid = {25630509} } @@ -3987,6 +4161,7 @@ @article{Lerch:2015:PNAS keywords = {conformational exchange,DEER,EPR,protein structural dynamics}, pages = {E2437--E2446}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/CGCRGI3E/Lerch et al. - 2015 - Structure-relaxation mechanism for the response of.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/F5EW9I4N/E2437.html:text/html}, + groups = {lysozyme}, pmid = {25918400} } @@ -4006,11 +4181,12 @@ @article{Maeno:2015:BiophysicalJournal year = {2015}, pages = {133--145}, file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/MCBSKB4I/Maeno et al. - 2015 - Cavity as a Source of Conformational Fluctuation a.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/UJKVJJ4Q/S0006-3495(14)01196-5.html:text/html}, + groups = {lysozyme}, pmid = {25564860} } @article{Parker:2000:JournalofMolecularBiology, - title = {A Statistical Appraisal of Native State Hydrogen Exchange Data: Evidence for a Burst Phase continuum?1}, + title = {A Statistical Appraisal of Native State Hydrogen Exchange Data: Evidence for a Burst Phase Continuum?1}, volume = {300}, issn = {0022-2836}, shorttitle = {A Statistical Appraisal of Native State Hydrogen Exchange Data}, @@ -4025,7 +4201,8 @@ @article{Parker:2000:JournalofMolecularBiology year = {2000}, keywords = {burst phases,folding intermediates,folding kinetics,hydrogen exchange,protein folding}, pages = {1361--1375}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3XWDDT8I/Parker and Marqusee - 2000 - A statistical appraisal of native state hydrogen e.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/IDAH96HE/S0022283600939226.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3XWDDT8I/Parker and Marqusee - 2000 - A statistical appraisal of native state hydrogen e.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/IDAH96HE/S0022283600939226.html:text/html}, + groups = {lysozyme} } @article{Bouvignies:2011:Nature, @@ -4045,7 +4222,8 @@ @article{Bouvignies:2011:Nature year = {2011}, keywords = {Biophysics,Chemistry,Structural biology}, pages = {111--114}, - file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/EE228QG7/Bouvignies et al. - 2011 - Solution structure of a minor and transiently form.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FQ82WBSI/nature10349.html:text/html} + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/EE228QG7/Bouvignies et al. - 2011 - Solution structure of a minor and transiently form.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/FQ82WBSI/nature10349.html:text/html}, + groups = {lysozyme} } @article{Collins:2007:JournalofMolecularBiology, @@ -4063,7 +4241,8 @@ @article{Collins:2007:JournalofMolecularBiology year = {2007}, keywords = {high pressure crystallography,protein,structural rigidity}, pages = {752--763}, - file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3D5GIIF4/Collins et al. - 2007 - Structural Rigidity of a Large Cavity-containing P.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BTPNWRAZ/S0022283606016962.html:text/html} + file = {ScienceDirect Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/3D5GIIF4/Collins et al. - 2007 - Structural Rigidity of a Large Cavity-containing P.pdf:application/pdf;ScienceDirect Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/BTPNWRAZ/S0022283606016962.html:text/html}, + groups = {lysozyme} } @misc{Mobley:2016:, @@ -4076,87 +4255,57 @@ @misc{Mobley:2016: year = {2016} } -@comment{jabref-meta: groupsversion:3;} +@article{Sherborne:2016:JComputAidedMolDes, + title = {Collaborating to Improve the Use of Free-Energy and Other Quantitative Methods in Drug Discovery}, + volume = {30}, + issn = {0920-654X, 1573-4951}, + doi = {10.1007/s10822-016-9996-y}, + abstract = {In May and August, 2016, several pharmaceutical companies convened to discuss and compare experiences with Free Energy Perturbation (FEP). This unusual synchronization of interest was prompted by Schr{\"o}dinger's FEP+ implementation and offered the opportunity to share fresh studies with FEP and enable broader discussions on the topic. This article summarizes key conclusions of the meetings, including a path forward of actions for this group to aid the accelerated evaluation, application and development of free energy and related quantitative, structure-based design methods.}, + language = {en}, + timestamp = {2017-04-26T23:30:40Z}, + number = {12}, + urldate = {2017-04-26}, + journal = {J Comput Aided Mol Des}, + author = {Sherborne, Bradley and Shanmugasundaram, Veerabahu and Cheng, Alan C. and Christ, Clara D. and DesJarlais, Renee L. and Duca, Jose S. and Lewis, Richard A. and Loughney, Deborah A. and Manas, Eric S. and McGaughey, Georgia B. and Peishoff, Catherine E. and van Vlijmen, Herman}, + month = dec, + year = {2016}, + pages = {1139--1141}, + file = {Full Text PDF:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/RP3BP78U/Sherborne et al. - 2016 - Collaborating to improve the use of free-energy an.pdf:application/pdf;Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/XQFGQNPH/s10822-016-9996-y.html:text/html} +} + +@article{Aldeghi:2017:J.Am.Chem.Soc., + title = {Predictions of {{Ligand Selectivity}} from {{Absolute Binding Free Energy Calculations}}}, + volume = {139}, + issn = {0002-7863}, + doi = {10.1021/jacs.6b11467}, + abstract = {Binding selectivity is a requirement for the development of a safe drug, and it is a critical property for chemical probes used in preclinical target validation. Engineering selectivity adds considerable complexity to the rational design of new drugs, as it involves the optimization of multiple binding affinities. Computationally, the prediction of binding selectivity is a challenge, and generally applicable methodologies are still not available to the computational and medicinal chemistry communities. Absolute binding free energy calculations based on alchemical pathways provide a rigorous framework for affinity predictions and could thus offer a general approach to the problem. We evaluated the performance of free energy calculations based on molecular dynamics for the prediction of selectivity by estimating the affinity profile of three bromodomain inhibitors across multiple bromodomain families, and by comparing the results to isothermal titration calorimetry data. Two case studies were considered. In the first one, the affinities of two similar ligands for seven bromodomains were calculated and returned excellent agreement with experiment (mean unsigned error of 0.81 kcal/mol and Pearson correlation of 0.75). In this test case, we also show how the preferred binding orientation of a ligand for different proteins can be estimated via free energy calculations. In the second case, the affinities of a broad-spectrum inhibitor for 22 bromodomains were calculated and returned a more modest accuracy (mean unsigned error of 1.76 kcal/mol and Pearson correlation of 0.48); however, the reparametrization of a sulfonamide moiety improved the agreement with experiment.}, + timestamp = {2017-04-26T23:34:45Z}, + number = {2}, + urldate = {2017-04-26}, + journal = {J. Am. Chem. Soc.}, + author = {Aldeghi, Matteo and Heifetz, Alexander and Bodkin, Michael J. and Knapp, Stefan and Biggin, Philip C.}, + month = jan, + year = {2017}, + keywords = {absolute binding free energy,alchemical,bromodomains}, + pages = {946--957}, + file = {ACS Full Text PDF w/ Links:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/M53IS5VD/Aldeghi et al. - 2017 - Predictions of Ligand Selectivity from Absolute Bi.pdf:application/pdf;ACS Full Text Snapshot:/Users/dmobley/Library/Application Support/Zotero/Profiles/i2jd8b87.default/zotero/storage/DUNNTPKW/jacs.html:text/html}, + groups = {bromodomains} +} + +@comment{jabref-meta: databaseType:bibtex;} @comment{jabref-meta: groupstree: 0 AllEntriesGroup:; -1 ExplicitGroup:bromodomains\;0\;aldeghi_accurate_2016\;Filippakopoulo -s:2010:Nature\;Chung:2011:J.Med.Chem.\;Hewings:2012:J.Med.Chem.\;Bambo -rough:2015:J.Med.Chem.\;Ran:2015:J.Med.Chem.\;Zhang:2013:J.Med.Chem.\; -Gosmini:2014:J.Med.Chem.\;Yang:2016:BioorganicChemistry\;; 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The right to create derivative works is also executed here with permission from the \emph{Annual Review of Biophysics}.} + \end{abstract} + \maketitle @@ -88,7 +94,7 @@ \section{INTRODUCTION} Molecular simulations provide a powerful technique for predicting and understanding the structure, function, dynamics, and interactions of biomolecules. -Often, these techniques are valued because they provide a movie of what might be going on at the atomic level. +Often, these techniques are valued because they provide a way to actually watch what might be going on at the atomic level. However, simulations also can be used to make quantitative predictions of thermodynamic and kinetic properties, with applications in fields including drug discovery, chemical engineering, and nanoengineering. A thermodynamic property of particular interest is the binding affinity between biomolecules and ligands such as inhibitors, modulators, or activators. With accurate and rapid affinity predictions, we could use simulations in varied health-related applications, such as the prediction of biomolecular interaction networks in support of systems biology, or rapid design of new medications with reduced side-effects and drug resistance. @@ -103,12 +109,12 @@ \subsection{Imagining a tool for drug discovery} If synthesizing and testing each compound takes several days, this workflow compresses roughly a year's work into a few days. -While this workflow is not yet a reality, huge strides have been made in this direction, with calculated binding affinity predictions now showing real promise~\cite{mobley_perspective_2012, christ_accuracy_2014, deng_distinguishing_2015, sherborne_preprint_2016, schrodinger_accurate_2015, christ_binding_2016, cui_affinity_2016, verras_free_2016}, solubility predictions beginning to come online~\cite{Schnieders:2012:J.Chem.TheoryComput., park_absolute_2014, liu_using_2016}, and predicted drug resistance/selectivity also apparently tractable~\cite{leonis_contribution_2013, leonis_contribution_2013}, with some headway apparent on membrane permeability~\cite{lee_permeability_2016, comer_permeability_2014}. -A considerable amount of science and engineering still remains to make this vision a reality, but, given recent progress, the question now seems more one of \emph{when} rather than \emph{whether}. +While this workflow is not yet a reality, huge strides have been made in this direction, with calculated binding affinity predictions now showing real promise~\cite{mobley_perspective_2012, christ_accuracy_2014, deng_distinguishing_2015, Sherborne:2016:JComputAidedMolDes, schrodinger_accurate_2015, christ_binding_2016, cui_affinity_2016, verras_free_2016}, solubility predictions beginning to come online~\cite{Schnieders:2012:J.Chem.TheoryComput., park_absolute_2014, liu_using_2016}, and predicted drug resistance/selectivity also apparently tractable~\cite{leonis_contribution_2013, leonis_contribution_2013}, with some headway apparent on membrane permeability~\cite{lee_permeability_2016, comer_permeability_2014}. +A considerable amount of science and engineering still remains to be done to make this vision a reality, but, given recent progress, the question now seems more one of \emph{when} rather than \emph{whether}. \subsection{Increasing accuracy will yield increasing payoffs} -Recent progress in computational power, especially the widespread availability of graphics processing units (GPUs) and advances in automation~\cite{liu_lead_2013} and sampling protocols, have helped simulation-based techniques reach the point where they now appear to have sufficient accuracy to be genuinely useful in guiding pharmaceutical drug discovery, at least for a certain subset of problems~\cite{mikulskis_large-scale_2014, homeyer_binding_2014, sherborne_preprint_2016, schrodinger_accurate_2015, christ_binding_2016, cui_affinity_2016, verras_free_2016}. +Recent progress in computational power, especially the widespread availability of graphics processing units (GPUs) and advances in automation~\cite{liu_lead_2013} and sampling protocols, have helped simulation-based techniques reach the point where they now appear to have sufficient accuracy to be genuinely useful in guiding pharmaceutical drug discovery, at least for a certain subset of problems~\cite{mikulskis_large-scale_2014, homeyer_binding_2014, Sherborne:2016:JComputAidedMolDes, schrodinger_accurate_2015, christ_binding_2016, cui_affinity_2016, verras_free_2016}. Specifically, in some situations, free energy calculations appear to be capable of achieving RMS errors in the 1-2 kcal/mol range with current force fields, even in prospective applications. As a consequence, pharmaceutical companies are beginning to use these methods in discovery projects. The most immediate application of these techniques is to guide synthesis for lead optimization, but applications to scaffold hopping and in other areas also appear possible. @@ -131,7 +137,7 @@ \subsection{Overview of free energy calculations} In either case, the energy of a given configuration is provided by a potential function, or force field, which estimates the potential energy of a system of solute and solvent molecules as a function of the coordinates of all of its atoms. Such simulations may be used in several different ways to compute binding free energies or relative binding free energies, as detailed elsewhere~\cite{michel_prediction_2010, christ_basic_2010, chodera_alchemical_2011, shirts_introduction_2013} and summarized below. In all cases, however, the calculations yield the free energy difference between two states of a molecular system, and they do so by computing the reversible work for changing the initial state to the final one. Two broad approaches deserve mention. -The first general approach directly computes the standard free energy of binding of two molecules via evaluating the reversible work of transferring the ligand from the binding site into solution. +The first general approach directly computes the standard binding free energy of two molecules via evaluating the reversible work of transferring the ligand from the binding site into solution. (This is sometimes called an absolute binding free energy calculation.) The pathway of this change may be one that is physically realizable, or one that is only realizable {\em in silico}, in which case it is sometimes called an ``alchemical'' pathway. Physical pathway methods provide the standard binding free energy by computing the reversible work of, in effect, pulling the ligand out of the binding site. @@ -191,7 +197,7 @@ \subsection{Improving modeling by cycles of testing, prediction, and improvement SAMPL, in contrast, focuses on predictions in simpler physical settings~\cite{Mobley:2016:}, such as small molecules in aqueous and organic phases, and small molecules binding to supramolecular hosts. Together, the SAMPL and D3R challenges roughly span the spectrum from properties we can predict now (though they may be challenging in some cases~\cite{bannan_blind_2016, yin_overview_2016, Mobley:2016:}) to the drug binding we want to be able to reliably predict. These challenges are vital as they provide our only opportunity, at present, to routinely see how different methods compare when attempting to compute the same properties, and they provide the beginnings of a model for how we can best advance free energy techniques: routinely testing our methods on the same, well-understood systems to learn what does and doesn't work to improve performance. -Thus, we need not just blind tests, but retrospective testing on well-understood, ``benchmark'' systems, detailed below. +Thus, we need not just blind tests, but retrospective testing on well-understood, ``benchmark'' systems. \section{THE NEED FOR WELL-CHOSEN BENCHMARK SYSTEMS} @@ -216,7 +222,7 @@ \subsubsection{Hard benchmarks} It is crucial yet nontrivial to validate that a simulation package correctly implements and applies the desired methods~\cite{shirts_lessons_2016}, and benchmark cases can help with this. First, all software packages could be tested for their ability to generate correct potential energies for a single configuration of a specified molecular system and force field. These results should be correct to within rounding error and the precision of the physical constants used in the calculations~\cite{shirts_lessons_2016}. -Similarly, different methods and software packages should give consistent binding free energies when identical force fields are applied with identical simulation setups and compositions. +Second, different methods and software packages should give consistent binding free energies when identical force fields are applied with identical simulation setups and compositions. The benchmark systems for such testing can be simple and easy to converge, and high precision free energies (e.g., uncertainty $\approx 0.1$ kcal/mol) should serve as a reference. Test calculations should typically agree with reference results to within 95\% confidence intervals, from established methods~\cite{shirts_statistically_2008,flyvbjerg_error_1989}, For this purpose, the correctly computed values need not agree with experiment; indeed, experimental results are unnecessary. @@ -265,7 +271,7 @@ \subsubsection{Soft benchmarks} \item System challenges \begin{enumerate} \item Protonation state of ligand and/or protein changes on binding - \item Multiple protonation states of the ligand and/or receptor are relevant, due to pKas near the experimental pH, or the presence of multiple relevant tautomers + \item Multiple protonation states of the ligand and/or receptor are relevant, due to $pK_a$s near the experimental pH, or the presence of multiple relevant tautomers \item Results are sensitive to buffer, salts or other environmental factors \end{enumerate} \item Force field challenges @@ -381,7 +387,7 @@ \subsubsection{Cucurbiturils} %Force field -Despite these issues, CB7 appears to be at the point where careful studies can probe the true accuracy of our force fields~\cite{hsiao_prediction_2014, muddana_prediction_2012,henriksen_computational_2015, gao_binding_2015, yin_toward_2015}, and the results can be sobering, with RMS errors in the binding free energies as high as 8 kcal/mol~\cite{henriksen_computational_2015, monroe_converging_2014}. +Despite these issues, CB7 appears to be at the point where careful studies can probe the true accuracy of our force fields~\cite{hsiao_prediction_2014, muddana_prediction_2012,henriksen_computational_2015, gao_binding_2015, yin_toward_2015}, and the results can be sobering, with root mean square (RMS) errors in the binding free energies as high as 8 kcal/mol~\cite{henriksen_computational_2015, monroe_converging_2014}. More encouragingly, the values of $R^2$ values can be as high as 0.92~\cite{henriksen_computational_2015}. Calculated values are in many cases quite sensitive to details of force field parameters~\cite{monroe_converging_2014, moghaddam_new_2011, muddana_prediction_2012}. For example, modest modification of some Lennard-Jones parameters yielded dramatic improvements in calculated values~\cite{yin_toward_2015}, and host-guest binding data has, accordingly, been suggested as an input for force field development~\cite{yin_toward_2015, henriksen_computational_2015, gao_binding_2015}. Water structure around CB7 and calculated binding enthalpies also appear particularly sensitive to the choice of water model~\cite{rogers_role_2013, fenley_bridging_2014, gao_binding_2015}, and water is clearly important for modulating binding~\cite{nguyen_grid_2012}. @@ -432,13 +438,13 @@ \subsubsection{Cucurbiturils} \toprule \multicolumn{1}{c}{ID$^{\rm a}$} & \multicolumn{1}{c}{name} & \multicolumn{1}{c}{PC CID$^{\rm b}$} & \multicolumn{1}{c}{2D} & \multicolumn{1}{c}{\rmfamily SMILES} & \multicolumn{1}{c}{$\Delta G^{\rm c,d}$ \,{(}kcal/mol{)}} \\ \midrule -2 & dopamine & 681 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/681.pdf}} & C1=CC(=C(C=C1CCN)O)O & -6.31 \pm 0.05 \\ -4 & o-phenylenediamine & 7243 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7243.pdf}} & C1=CC=C(C(=C1)N)N & -6.68 \pm 0.05 \\ -5 & m-phenylenediamine & 7935 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7935.pdf}} & C1=CC(=CC(=C1)N)N & -6.69 \pm 0.02 \\ -7 & 4-(aminomethyl)pyridine & 77317 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/77317.pdf}} & C1=CN=CC=C1CN & -7.56 \pm 0.06 \\ -8 & p-phenylenediamine & 7814 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7814.pdf}} & C1=CC(=CC=C1N)N & -8.60 \pm 0.06 \\ -9 & p-toluidine & 7813 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7813.pdf}} & CC1=CC=C(C=C1)N & -9.43 \pm 0.05 \\ -20 & p-xylylenediamine & 68315 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/68315.pdf}} & C1=CC(=CC=C1CN)CN & -12.62 \pm 0.06 \\ +2 & dopamine & 681 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/681.pdf}} & c1cc(c(cc1CCN)O)O & -6.31 \pm 0.05 \\ +4 & o-phenylenediamine & 7243 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7243.pdf}} & c1ccc(c(c1)N)N & -6.68 \pm 0.05 \\ +5 & m-phenylenediamine & 7935 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7935.pdf}} & c1cc(cc(c1)N)N & -6.69 \pm 0.02 \\ +7 & 4-(aminomethyl)pyridine & 77317 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/77317.pdf}} & c1cnccc1CN & -7.56 \pm 0.06 \\ +8 & p-phenylenediamine & 7814 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7814.pdf}} & c1cc(ccc1N)N & -8.60 \pm 0.06 \\ +9 & p-toluidine & 7813 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7813.pdf}} & Cc1ccc(cc1)N & -9.43 \pm 0.05 \\ +20 & p-xylylenediamine & 68315 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/68315.pdf}} & c1cc(ccc1CN)CN & -12.62 \pm 0.06 \\ \bottomrule \end{tabular} \\ $^{\rm a}$ Compound ID from original paper; $^{\rm b}$ PubChem Compound ID; $^{\rm c}$ Standard binding free energy, where all measurements were done via NMR in 50mM sodium acetate buffer in $D_2O$ at pH 4.74 and 298 K. Uncertainties are obtained by taking the reported standard deviations across triplicate measurements~\cite{isaacs_personal_2016} and dividing by $\sqrt 3$; $^{\rm d}$ drawn from~\cite{liu_cucurbituril_2005}. @@ -463,7 +469,7 @@ \subsubsection{Gibb Deep Cavity Cavitands (GDCC)} The octa-acids tend to bind guest molecules possessing a hydrophobic moiety that fits into the host's cavity and a hydrophilic moiety that projects into the aqueous solvent. Within these specifications, they bind a diversity of ligands, including both organic cations and anions, as well as neutral compounds with varying degrees of polarity~\cite{gibb_guests_2009, gibb_binding_2013}. Compounds with adamantane or noradamantane groups display perhaps the highest affinities observed so far, with binding free energies ranging to about -8 kcal/mol~\cite{sun_calorimetric_2008}. -Much of the experimental binding data comes from ITC, so binding enthalpies are often available. +Many of the experimental binding data comes from ITC, so binding enthalpies are often available. Two experimental aspects of binding are particularly intriguing and noteworthy. First, the binding thermodynamics of OA is sensitive to the type and concentration of anions in solution. @@ -497,7 +503,7 @@ \subsubsection{Gibb Deep Cavity Cavitands (GDCC)} \item{{\bf Finite-size artifacts due to charge modification}: As for CB7, it should be ascertained that calculations in which charged guests are decoupled from the system do not generate artifacts related to long range Coulomb interactions.~\cite{rocklin_calculating_2013, lin_overview_2014, reif_net_2014, simonson_concepts_2016}.} -\item{{\bf Protonation state effects}: Although experiments are typically run at pH values that lead to well-defined protonation states of the host and its guests, this may not always hold~\cite{muddana_sampl4_2014, ewell_water_2008, tofoleanu_absolute_2016}, particularly given experimental evidence for extreme binding-driven pKa shifts of 3-4 log units for some carboxylate compounds~\cite{wang_itc_2016, sokkalingam_binding_2016}. +\item{{\bf Protonation state effects}: Although experiments are typically run at pH values that lead to well-defined protonation states of the host and its guests, this may not always hold~\cite{muddana_sampl4_2014, ewell_water_2008, tofoleanu_absolute_2016}, particularly given experimental evidence for extreme binding-driven $pK_a$ shifts of 3-4 log units for some carboxylate compounds~\cite{wang_itc_2016, sokkalingam_binding_2016}. Thus, attention should be given to ionization states and their modulation by binding.} \end{enumerate} @@ -516,17 +522,17 @@ \subsubsection{Gibb Deep Cavity Cavitands (GDCC)} \multicolumn{8}{c}{OA host} \\ \midrule 3 & OA-G1 & 5-hexynoic acid & 143036 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/143036.pdf}} & C\#CCCCC(=O)O & -5.40 \pm 0.003 & -7.71 \pm 0.05 \\ -4 & OA-G6 & 3-nitrobenzoic acid & 8497 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/8497.pdf}} & C1=CC(=CC(=C1)[N+](=O)[O-])C(=O)O & -5.34 \pm 0.005 & -5.67 \pm 0.01 \\ -5 & OA-G2 & 4-cyanobenzoic acid & 12087 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/12087.pdf}} & C1=CC(=CC=C1C\#N)C(=O)O & -4.73 \pm 0.01 & -4.45 \pm 0.08 \\ +4 & OA-G6 & 3-nitrobenzoic acid & 8497 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/8497.pdf}} & c1cc(cc(c1)[N+](=O)[O-])C(=O)O & -5.34 \pm 0.005 & -5.67 \pm 0.01 \\ +5 & OA-G2 & 4-cyanobenzoic acid & 12087 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/12087.pdf}} & c1cc(ccc1C\#N)C(=O)O & -4.73 \pm 0.01 & -4.45 \pm 0.08 \\ 6 & OA-G4 & 4-bromoadamantane-1-carboxylic acid & 12598766 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/12598766.pdf}} & C1C2CC3CC(C2)(CC1C3Br)C(=O)O & -9.37 \pm 0.01 & -14.78 \pm 0.02 \\ 7 & OA-G3 & N,N,N-trimethylhexan-1-aminium & 84774 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/84774.pdf}} & CCCCCC[N+](C)(C)C & -4.49 \pm 0.01 & -5.91 \pm 0.10 \\ -8 & OA-G5 & trimethylphenethylaminium & 14108 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/14108.pdf}} & C[N+](C)(C)CCC1=CC=CC=C1 & -3.72 \pm 0.01 & -9.96 \pm 0.11 \\ +8 & OA-G5 & trimethylphenethylaminium & 14108 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/14108.pdf}} & Cc1ccccc1CC(C)(C)[NH3+] & -3.72 \pm 0.01 & -9.96 \pm 0.11 \\ \midrule \multicolumn{8}{c}{TEMOA/OAMe host} \\ \midrule 3 & OA-G1 & 5-hexynoic acid & 143036 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/143036.pdf}} & C\#CCCCC(=O)O & -5.476 \pm 0.006 & -9.961 \pm 0.006 \\ -4 & OA-G6 & 3-nitrobenzoic acid & 8497 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/8497.pdf}} & C1=CC(=CC(=C1)[N+](=O)[O-])C(=O)O & -4.52 \pm 0.02 & -9.1 \pm 0.1 \\ -5 & OA-G2 & 4-cyanobenzoic acid & 12087 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/12087.pdf}} & C1=CC(=CC=C1C\#N)C(=O)O & -5.26 \pm 0.01 & -7.6 \pm 0.1 \\ +4 & OA-G6 & 3-nitrobenzoic acid & 8497 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/8497.pdf}} & c1cc(cc(c1)[N+](=O)[O-])C(=O)O & -4.52 \pm 0.02 & -9.1 \pm 0.1 \\ +5 & OA-G2 & 4-cyanobenzoic acid & 12087 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/12087.pdf}} & c1cc(ccc1C\#N)C(=O)O & -5.26 \pm 0.01 & -7.6 \pm 0.1 \\ 7 & OA-G3 & N,N,N-trimethylhexan-1-aminium & 84774 & \parbox[c]{1em}{\includegraphics[scale=0.15]{figures/84774.pdf}} & CCCCCC[N+](C)(C)C & -5.73 \pm 0.06 & -6.62 \pm 0.2 \\ \bottomrule \end{tabular}\\ @@ -544,11 +550,11 @@ \subsubsection{Gibb Deep Cavity Cavitands (GDCC)} \toprule \multicolumn{1}{c}{ID$^{\rm a}$} & \multicolumn{1}{c}{name} & \multicolumn{1}{c}{PC CID$^{\rm b}$} & \multicolumn{1}{c}{2D} & \multicolumn{1}{c}{\rmfamily SMILES} & \multicolumn{1}{c}{Method} & \multicolumn{1}{c}{$\Delta G^{\rm c}$ \,{(}kcal/mol{)}} \\ \midrule -1 & benzoic acid & 243 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/243.pdf}} & C1=CC=C(C=C1)C(=O)O & NMR & -3.72 \pm 0.03 \\ -2 & 4-methylbenzoic acid & 7470 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7470.pdf}} & CC1=CC=C(C=C1)C(=O)O & NMR & -5.85 \pm 0.06 \\ -3 & 4-ethylbenzoic acid & 12086 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/12086.pdf}} & CCC1=CC=C(C=C1)C(=O)O & ITC & -6.27 \pm 0.01 \\ -4 & 4-chlorobenzoic acid & 6318 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/6318.pdf}} & C1=CC(=CC=C1C(=O)O)Cl & ITC & -6.72 \pm 0.01 \\ -5 & 3-chlorobenzoic acid & 447 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/447.pdf}} & C1=CC(=CC(=C1)Cl)C(=O)O & NMR & -5.24 \pm 0.02 \\ +1 & benzoic acid & 243 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/243.pdf}} & c1ccc(cc1)C(=O)O & NMR & -3.72 \pm 0.03 \\ +2 & 4-methylbenzoic acid & 7470 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7470.pdf}} & Cc1ccc(cc1)C(=O)O & NMR & -5.85 \pm 0.06 \\ +3 & 4-ethylbenzoic acid & 12086 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/12086.pdf}} & CCc1ccc(cc1)C(=O)O & ITC & -6.27 \pm 0.01 \\ +4 & 4-chlorobenzoic acid & 6318 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/6318.pdf}} & c1cc(ccc1C(=O)O)Cl & ITC & -6.72 \pm 0.01 \\ +5 & 3-chlorobenzoic acid & 447 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/447.pdf}} & c1cc(cc(c1)Cl)C(=O)O & NMR & -5.24 \pm 0.02 \\ 6 & cyclohexanecarboxylic acid & 7413 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/7413.pdf}} & C1CCC(CC1)C(=O)O & NMR & -5.62 \pm 0.04 \\ 7 & trans-4-methylcyclohexanecarboxylic acid & 20330 & \parbox[c]{1em}{\includegraphics[scale=0.2]{figures/20330.pdf}} & [C@@H]1(CC[C@@H](CC1)C(=O)O[H])C & ITC & -7.61 \pm 0.04 \\ \bottomrule @@ -569,8 +575,8 @@ \subsubsection{Gibb Deep Cavity Cavitands (GDCC)} Some salts even bind to OA themselves, with perchlorate~\cite{gibb_anion_2011} and trichloroacetate~\cite{sokkalingam_binding_2016} being particularly potent, and thus will compete with guests for binding. Computationally, including additional salt beyond that needed for system neutralization changed binding free energies by up to 4 kcal/mol~\cite{tofoleanu_absolute_2016}. -Although the protonation states of the guests might seem clear and unambiguous, experimental evidence also indicates major pKa shifts on binding so that species such as acetate, formate and others could bind in neutral form at neutral pH~\cite{wang_itc_2016, sokkalingam_binding_2016}. -One study used absolute binding free energy calculations for different guest charge states, coupled with pKa calculations, and found that inclusion of pKa corrections and the possibility of alternate charge states of the guests affected calculated binding free energies by up to 2 kcal/mol~\cite{tofoleanu_absolute_2016}. +Although the protonation states of the guests might seem clear and unambiguous, experimental evidence also indicates major $pK_a$ shifts on binding so that species such as acetate, formate and others could bind in neutral form at neutral pH~\cite{wang_itc_2016, sokkalingam_binding_2016}. +One study used absolute binding free energy calculations for different guest charge states, coupled with $pK_a$ calculations, and found that inclusion of $pK_a$ corrections and the possibility of alternate charge states of the guests affected calculated binding free energies by up to 2 kcal/mol~\cite{tofoleanu_absolute_2016}. Even the host protonation state may be unclear. Although OA might be assumed to have all eight carboxylic acids deprotonated at the basic pH of typical experiments, the four at the bottom are in close proximity, and these might make hydrogen bonds allowing retention of two protons~\cite{ewell_water_2008}. Thus, there are uncertainties as to the host protonation state~\cite{muddana_sampl4_2014, ewell_water_2008}, which perhaps also could be modulated by guest binding. @@ -608,7 +614,7 @@ \subsection{Protein-ligand benchmarks: the T4 lysozyme model binding sites} The utility of the lysozyme model sites is also driven by the large body of available experimental data. It has been relatively easy to identify new ligands and obtain high quality crystal structures and affinity measurements, and this has allowed two different rounds of blinded free energy prediction exercises~\cite{mobley_predicting_2007, boyce_predicting_2009}. -These binding sites do exhibit some surprising experimental complexities which make them interesting ongoing topics of study, such as the fact that the L99A site is empty of water when ligands are not bound~\cite{Nucci:2014:PNAS, Lerch:2015:PNAS, Collins:2007:JournalofMolecularBiology} yet the protein can undergo pressure-induced filing~\cite{Collins:2007:JournalofMolecularBiology,Lerch:2015:PNAS} or denaturation~\cite{Nucci:2014:PNAS} which can be inhibited by binding of ligand~\cite{Nucci:2014:PNAS, Lerch:2015:PNAS}. +These binding sites do exhibit some surprising experimental complexities which make them interesting ongoing topics of study, such as the fact that the L99A site is empty of water when ligands are not bound~\cite{Nucci:2014:PNAS, Lerch:2015:PNAS, Collins:2007:JournalofMolecularBiology} yet the protein can undergo pressure-induced filling~\cite{Collins:2007:JournalofMolecularBiology,Lerch:2015:PNAS} or denaturation~\cite{Nucci:2014:PNAS} which can be inhibited by binding of ligand~\cite{Nucci:2014:PNAS, Lerch:2015:PNAS}. Pressure may also cause the protein to populate an excited state~\cite{Maeno:2015:BiophysicalJournal, Kitahara:2015:PNAS} (but see~\cite{Wand:2015:PNAS}) which is already present to a very limited extent at equilibrium~\cite{Bouvignies:2011:Nature}. Still, as noted below, these issues do not seem to dramatically impact our ability to calculate binding free energies at standard temperature and pressure, probably in large part because these are effects which come into play only at high pressures~\cite{Nucci:2014:PNAS, Lerch:2015:PNAS, Maeno:2015:BiophysicalJournal}, though as we discuss below, some ligands do induce a protein conformational change which affects the same helix as the proposed excited state~\cite{merski_homologous_2015}. It seems likely that the conformational hetereogeneity observed experimentally will make lysozyme even more of a valuable benchmark system as test cases here can range from simple to challenging depending on the ligand and pressure being considered. @@ -728,8 +734,6 @@ \subsubsection{Computational challenges posed by the T4 lysozyme benchmarks} While sidechain sampling has been a significant challenge, it is possible to use biased sampling techniques such as umbrella sampling to deliberately compute and include free energies of sampling slow sidechain rearrangements~\cite{mobley_confine_2007}. However, this is not a general solution, since it requires knowing what sidechains might rearrange on binding and then expending substantial computational power to map the free energy landscapes for these rearrangements. An apparently better general strategy is including sidechains in enhanced sampling regions selected for Hamiltonian exchange~\cite{jiang_free_2010, khavrutskii_improved_2011} or REST2~\cite{wang_achieving_2012}, {\bf allowing sidechains to be alchemically softened or torsion barriers lowered (or both), to enhance sampling at alchemical intermediate states}. -%{\bf I don't understand the bolded text. For one thing, my impression is that REST only modifies T, and leaves the Hamiltonian unchanged.} -% DLM: REST2 -- which is what they currently use -- they like to describe as modifying T of a "local region" but really it's just modifying the Hamiltonian for selected residues, so it's a type of Hamiltonian exchange. You pick sidechains with interactions you want to soften, alchemically, and the softening is done at intermediate lambda values. How would you suggest clarifying the phrasing? (If my explanation is still unclear we could discuss on Slack or on the phone.) Reduction of energy barriers at intermediate $\lambda$ states in this scheme allows enhanced conformational sampling at these $\lambda$ values. Then, with swaps between $\lambda$ values, enhanced sidechain sampling at intermediate states can propagate to all states, improving convergence~\cite{jiang_free_2010, wang_achieving_2012}. @@ -807,15 +811,22 @@ \subsubsection{Bromodomain proteins} Bromodomains (BRDs) are a family of protein domains of about 100 residues that bind actylated lysine residues at the surface of histones and thus read out epigenetic markers. Bromodomains are present in many human proteins, and are being explored as potential drug targets for diseases including cancer and atherosclerosis~\cite{aldeghi_accurate_2016}. These compact domains can be expressed, purified and studied as independent proteins, and are associated with a growing body of small molecule binding data \cite{Filippakopoulos:2010:Nature, Chung:2011:J.Med.Chem., Hewings:2012:J.Med.Chem., Bamborough:2015:J.Med.Chem., Ran:2015:J.Med.Chem., Zhang:2013:J.Med.Chem., Gosmini:2014:J.Med.Chem., Yang:2016:BioorganicChemistry}, including some obtained by isothermal titration calorimetry \cite{Filippakopoulos:2010:Nature, Chung:2011:J.Med.Chem., Hewings:2012:J.Med.Chem., Gosmini:2014:J.Med.Chem.}. -%DLM: Contact Aldeghi, etc. for updates (new cite forthcoming?) -- waiting for response The small size of bromodomains, and the fact that their binding sites are relatively solvent-exposed, makes them particularly suitable for free energy simulations. One recent study, which used alchemical techniques to compute absolute binding free energies of 11 different ligands for bromodomain BRD4~\cite{aldeghi_accurate_2016}, achieved a remarkable level of accuracy, RMS error $0.8\pm0.2$ kcal/mol, for binding free energies spanning a range of \~4 kcal/mol. Docking calculations included in the same study did not work as well. The compounds studied were diverse, and therefore not amenable to relative free energy methods in which one ligand is computationally converted into another. -Overall, then, this appears to be class of systems that could yield relatively tractable and informative protein-ligand benchmark systems. -One known challenge is that some ligands have multiple plausible binding modes \cite{aldeghi_accurate_2016}. - In addition, a diverse ligand series can pose severe challenges for relative free energy techniques. + +An additional study applied absolute binding free energy calculations to compute the \emph{selectivity} of three different bromodomain inhibitors across a variety of different bromodomain families. +Affinities of two similar ligands for seven different bromodomains were computed with a mean unsigned error of just 0.81 kcal/mol and a Pearson correlation coefficient of 0.75. +Additionally, the affinity of a broad spectrum bromodomain inhibitor was calculated for some 22 different bromodomains with more modest accuracy. +Calculations also yielded insight into likely binding modes. +The affinity data for this case is high quality, all from ITC, and a variety of crystal structures are available, making this a potentially exciting benchmark for absolute binding free energy calculations~\cite{Aldeghi:2017:J.Am.Chem.Soc.}. + + +Overall, then, bromodomains appear to be class of systems that could yield relatively tractable and informative protein-ligand benchmark systems. +One known challenge is that some ligands have multiple plausible binding modes \cite{aldeghi_accurate_2016, Aldeghi:2017:J.Am.Chem.Soc.}. +In addition, a diverse ligand series (or binding to different proteins in a family!) can pose severe challenges for relative free energy techniques, meaning that bromodomains may perhaps be appealing primarily as a benchmark for absolute calculations, though perhaps suitable series for relative calculations may also be available. \subsubsection{Other protein-ligand systems}