Datasets and Jupyter notebook for the structural analysis of protein-RNA interface evolution

The present repository contains data and code related to our manuscript "Structural comparison of protein-RNA homologous interfaces reveals widespread overall conservation contrasted with versatility in polar contacts". In the manuscript, we analyze the evolution of protein-RNA interfaces by building a dataset of protein-RNA interologs (homologous interfaces) and exploring how interface contacts are conserved between homologous interfaces, as well as possible explanations for non-conserved contacts. This repository contains the following files: DataAnalysisNotebook.ipynb is a Jupyter notebook to reproduce contact conservation analysis and all figures from our manuscript 2022-02-21-PDB.csv contains data from the PDB about 3D structures of complexes containing interacting protein and RNA chains (PDB structure identifier, chain identifiers, experimental technique and resolution) 2022-02-21-PDB_proteinchainscontactingRNAchains.groupbp.tsv contains more detailed information about interacting protein and RNA chains from these complexes (PDB and chain identifiers, protein and RNA size, interface size and number of contacts) 2022-02-21-PDB_proteinchainscontactingRNAchains.groupbp.txt.selectXE_2.50_p30_r10_pi5_ri5_rep_bc-100.out_RNAcl_0.99.tsv contains the same detailed information, restricted to the filtered dataset used as a starting point in our interolog search pipeline PDBinterfaceAlign.csv contains information about the structural alignment of pairs of protein-RNA interactions (structural alignment TM-scores, sequence identity and coverage) DataInterologsParam.tsv contains information about a pre-filtered set of 2587 potential interologs (including interface RMSD, sequence identity and coverage and interface size) DataInterologsContacts.tsv contains detailed information about conserved and non-conserved contacts in the final set of 2022 interologs (atomic contacts, apolar contacts, hydrogen bonds, salt bridges and stacking information for aminoacid-nucleotide pairs, as well as information about whether each belongs to the interface, secondary structures, and the aminoacid surface accessibility and evolutionary conservation metrics) DataCons.csv contains precomputed contact conservation metrics for each of the 2022 interolog pairs, for fast reproduction of manuscript figures ListeIntraHbonds.pkl and ListeIntraSaltBridges.pkl are pickle-format data files containing intra-molecular hydrogen bonds and salt bridges (respectively) that are used to analyse scenarii of compensation for non-conserved polar contacts.