DOI: 10.5281/zenodo.17017952
title: Rotamer Libraries for RNA-Binding Proteins (RBPs) in Bound and Unbound States

description: Overview

This repository contains a comprehensive set of rotamer libraries for RNA-Binding Proteins (RBPs), specifically curated to analyze side-chain conformational preferences in the context of protein-RNA interactions. The libraries are stratified based on:





Backbone dependence: Backbone-Dependent (BBD) and Backbone-Independent (BBI) libraries.




Functional site: Residues at the RNA-binding interface (I) vs. non-interface (N) sites.




Functional state: Protein structures in the bound (B) and unbound (U) conformations.



These libraries are essential for computational structural biology, particularly in improving the accuracy of protein-RNA docking, side-chain packing prediction, and molecular modeling tasks.

Key Features





State-Specific Data: Separate statistics for bound and unbound protein conformations.




Spatially Resolved: Distinct data for interface and non-interface residues.




Statistically Robust: Probabilities and side-chain dihedral angles (χ) are provided as weighted circular means and standard deviations.



Dataset Structure and File Descriptions

The dataset is organized into two main catagories (with "bbd" for backbone dependent and "bbi" for backbone independent rotamers):

RBPs_rotamer_libraries/ ├── 1_BBD_rotamer_lib/ # Backbone-Dependent Library │ ├── RBPs_I_bbd_B_rotamer_lib.csv # Interface, Bound │ ├── RBPs_I_bbd_U_rotamer_lib.csv # Interface, Unbound │ ├── RBPs_N_bbd_B_rotamer_lib.csv # Non-Interface, Bound │ ├── RBPs_N_bbd_U_rotamer_lib.csv # Non-Interface, Unbound │ ├── RBPs_bbd_B_rotamer_lib.csv # Overall, Bound │ └── RBPs_bbd_U_rotamer_lib.csv # Overall, Unbound └── 2_BBI_rotamer_lib/ # Backbone-Independent Library ├── RBPs_I_bbi_B_rotamer_lib.csv # Interface, Bound ├── RBPs_I_bbi_U_rotamer_lib.csv # Interface, Unbound ├── RBPs_N_bbi_B_rotamer_lib.csv # Non-Interface, Bound ├── RBPs_N_bbi_U_rotamer_lib.csv # Non-Interface, Unbound ├── RBPs_bbi_B_rotamer_lib.csv # Overall, Bound └── RBPs_bbi_U_rotamer_lib.csv # Overall, Unbound

Backbone-Dependent (BBD) Library Columns

Each row corresponds to a specific (φ, ψ) bin.






Column Name
Description




AA
Amino acid type (3-letter code).


PHI
Backbone φ torsion angle (center of bin, in degrees).


PSI
Backbone ψ torsion angle (center of bin, in degrees).


_Count
Number of data points in this specific (φ, ψ) bin.


Count
Total number of data points in the (φ, ψ) neighborhood used for smoothing.


Prob
Probability of the rotamer in this bin (range 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) Library Columns

Each row provides global statistics for an amino acid type.






Column Name
Description




AA
Amino acid type (3-letter code).


Count
Total number of data points for this amino acid.


Prob
Normalized probability of occurrence (range 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).







Generation Methodology

These libraries were constructed from a high-quality, non-redundant set of protein-RNA complexes and their corresponding unbound structures. The methodology is based on established practices in rotamer library development:





Data Curation: Structures were sourced from the Protein-RNA Docking Benchmark v3.0.




Interface Definition: Residues were classified as interface (I) or non-interface (N) based on solvent accessibility changes and distance criteria to RNA upon binding.




Dihedral Calculation: Side-chain χ angles were calculated and binned.




Statistical Smoothing: Probabilities, circular means, and standard deviations were calculated using adaptive kernel density estimates and methods from circular statistics.



Notes





All angular measurements are in degrees.




Probability values (Prob) range from 0.0 (never observed) to 1.0 (always observed).




Standard deviations are calculated using circular statistics methods suitable for angular data.




The "Overall" libraries (RBPs_bbd_*, RBPs_bbi_*) contain data from all residues, regardless of their interface classification.