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@bioexcel

BioExcel

Center of Excellence for Computational Biomolecular Research

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  1. biobb biobb Public

    Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.

    Python 50 8

  2. gromacs-docker gromacs-docker Public

    Dockerfile for GROMACS

    Dockerfile 44 19

  3. gromacs-2022-cp2k-tutorial gromacs-2022-cp2k-tutorial Public

    Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface

    Makefile 31 6

  4. cp2K_qmmm_tutorials_for_biological_simulations cp2K_qmmm_tutorials_for_biological_simulations Public

    Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.

    Jupyter Notebook 19 7

  5. biobb_structure_checking biobb_structure_checking Public

    Python 11 1

  6. pymdsetup pymdsetup Public

    Python 9 1

Repositories

Showing 10 of 118 repositories
  • biobb_mem Public
    bioexcel/biobb_mem’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Nov 11, 2024
  • biobb_chemistry Public

    Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.

    bioexcel/biobb_chemistry’s past year of commit activity
    Python 4 Apache-2.0 2 0 0 Updated Nov 8, 2024
  • biobb_adapters Public

    Biobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.

    bioexcel/biobb_adapters’s past year of commit activity
    Common Workflow Language 0 Apache-2.0 5 4 0 Updated Nov 6, 2024
  • utils_biobb Public
    bioexcel/utils_biobb’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Nov 6, 2024
  • biobb_pmx Public

    Biobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.

    bioexcel/biobb_pmx’s past year of commit activity
    Python 2 Apache-2.0 0 2 0 Updated Nov 4, 2024
  • biobb_vs Public

    Biobb_vs is the Biobb module collection to perform virtual screening studies.

    bioexcel/biobb_vs’s past year of commit activity
    Python 1 Apache-2.0 2 0 0 Updated Nov 4, 2024
  • biobb_godmd Public

    biobb_godmd is a BioBB category for the GOdMD tool

    bioexcel/biobb_godmd’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Nov 4, 2024
  • biobb_structure_utils Public

    Biobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues.

    bioexcel/biobb_structure_utils’s past year of commit activity
    Python 2 Apache-2.0 2 0 0 Updated Nov 4, 2024
  • biobb_pytorch Public

    Biobb_pytorch is the Biobb module collection to create and train ML & DL models using the popular PyTorch Python library.

    bioexcel/biobb_pytorch’s past year of commit activity
    Python 1 Apache-2.0 0 0 0 Updated Nov 4, 2024
  • biobb_io Public

    Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.

    bioexcel/biobb_io’s past year of commit activity
    Python 2 Apache-2.0 0 0 0 Updated Nov 4, 2024
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