RNA Binding Proteins (RBPs) Rotamer Libraries

📁 Directory Structure

 RBPs_rotamer_libraries/
├── RBPs_BBD_rotamer_lib/
│   ├── RBPs_I_bbd_B_rotamer_lib.csv
│   ├── RBPs_I_bbd_U_rotamer_lib.csv
│   ├── RBPs_N_bbd_B_rotamer_lib.csv
│   ├── RBPs_N_bbd_U_rotamer_lib.csv
│   ├── RBPs_bbd_B_rotamer_lib.csv
│   └── RBPs_bbd_U_rotamer_lib.csv
└── RBPs_BBI_rotamer_lib/
    ├── RBPs_I_bbi_B_rotamer_lib.csv
    ├── RBPs_I_bbi_U_rotamer_lib.csv
    ├── RBPs_N_bbi_B_rotamer_lib.csv
    ├── RBPs_N_bbi_U_rotamer_lib.csv
    ├── RBPs_bbi_B_rotamer_lib.csv
    └── RBPs_bbi_U_rotamer_lib.csv 

🌀 Backbone Dependent (BBD) Rotamer Library

File Descriptions

File Name	Description
RBPs_I_bbd_B_rotamer_lib.csv	Rotamers at the RNA-binding interface (I) in bound (B) conformation
RBPs_I_bbd_U_rotamer_lib.csv	Rotamers at the RNA-binding interface (I) in unbound (U) conformation
RBPs_N_bbd_B_rotamer_lib.csv	Rotamers at the non RNA-binding site (N) in bound (B) conformation
RBPs_N_bbd_U_rotamer_lib.csv	Rotamers at the non RNA-binding site (N) in unbound (U) conformation
RBPs_bbd_B_rotamer_lib.csv	Overall in bound (B) conformation
RBPs_bbd_U_rotamer_lib.csv	Overall in unbound (U) conformation

Column Descriptions

Column	Description
AA	Amino acid residue (3-letter code)
PHI	Backbone φ torsion angle (degrees)
PSI	Backbone ψ torsion angle (degrees)
_Count	Data points in specific (φ, ψ) bin
Count	Total data points in (φ, ψ) neighborhood
Prob	Probability of occurrence in bin (0.0-1.0)
B/U_CHI[1-4]	Bound/Unbound χₙ weighted circular mean (degrees)
B/U_CHI[1-4]Sig	Bound/Unbound χₙ weighted circular standard deviation (degrees)

📊 Backbone Independent (BBI) Rotamer Library

File Descriptions

File Name	Description
RBPs_I_bbi_B_rotamer_lib.csv	Interface (I) bound (B) residues - Backbone independent
RBPs_I_bbi_U_rotamer_lib.csv	Interface (I) unbound (U) residues - Backbone independent
RBPs_N_bbi_B_rotamer_lib.csv	Non-interface (N) bound (B) residues - Backbone independent
RBPs_N_bbi_U_rotamer_lib.csv	Non-interface (N) unbound (U) residues - Backbone independent
RBPs_bbi_B_rotamer_lib.csv	Overall bound (B) residues - Backbone independent
RBPs_bbi_U_rotamer_lib.csv	Overall unbound (U) residues - Backbone independent

Column Descriptions

Column	Description
AA	Amino acid residue (3-letter code)
Count	Total data points in bin
Prob	Probability of occurrence (0.0-1.0)
B/U_CHI[1-4]	Bound/Unbound χₙ weighted circular mean (degrees)
B/U_CHI[1-4]Sig	Bound/Unbound χₙ weighted circular standard deviation (degrees)

💻 Usage Example

📝 Notes

1. All angular measurements are in degrees
2. Probability values range from 0.0 (never observed) to 1.0 (always observed)
3. Standard deviations calculated using circular statistics methods
4. Interface/non-interface classification based on [reference to criteria]

🔗 References

1. Kant, S., Nithin, C., Mukherjee, S., Maity, A., Bahadur, R.P., 2025. Protein‐ RNA Docking Benchmark v3.0 Integrated With Binding Affinity. Proteins prot.26825. https://doi.org/10.1002/prot.26825

2. Lovell, S.C., Word, J.M., Richardson, J.S., Richardson, D.C., 2000. The penultimate rotamer library. Proteins 40, 389–408. https://doi.org/10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2

3. Shapovalov, M.V., Dunbrack, R.L., 2011. A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions. Structure 19, 844–858. https://doi.org/10.1016/j.str.2011.03.019

4. Dunbrack, R.L., Karplus, M., 1993. Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction. Journal of Molecular Biology 230, 543–574. https://doi.org/10.1006/jmbi.1993.1170

5. Zhang, O., Naik, S.A., Liu, Z.H., Forman-Kay, J., Head-Gordon, T., 2024. A curated rotamer library for common post-translational modifications of proteins. Bioinformatics 40. https://doi.org/10.1093/BIOINFORMATICS/BTAE444

6. Mardia, K.V., Zemroch, P.J., 1975. Algorithm AS 86: The Von Mises Distribution Function. Applied Statistics 24, 268. https://doi.org/10.2307/2346578

7. Mukherjee, S., Bahadur, R.P., 2018. An account of solvent accessibility in protein-RNA recognition. Sci Rep 8, 10546. https://doi.org/10.1038/s41598-018-28373-2

📄 License

[Please suggest the license type] @Sunandan Da

If you find this work and use it on your work please cite:

Sunandan Mukherjee, Shri Kant, and Ranjit P Bahadur. Transition of side-chain conformations of RNA-binding proteins upon bindng RNA (2026).