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, and to explore data env.yaml is an environment file in order to build a Conda/Mamba environment to run the Jupyter notebook 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) DataInterologsContactsFixedSASA.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) - compared to version 1, the calculation of solvent accessibility was fixed for a number of interolog pairs DataCons.csv contains precomputed contact conservation metrics for each of the 2022 interolog pairs, for fast reproduction of manuscript figures DataInterologsContactsResampledMaintainStructSeqId.tsv, DataInterologsContactsShuffled.tsv and DataInterologsShuffled.tsv relate to baselines computed for contact conservation assessment clan.txt, clan_membership.txt, ecod.latest.domains.uniq.txt, rfam_interfaces_977.txt, DataGroupsECOD.tsv, DataGroupesRFAM.tsv, DataGroupsRFAMClan.tsv, DataInterfaceGroupsECOD.tsv and DataInterfaceGroupsRFAM.tsv relate to the ECOD (respectively Rfam) classification of protein domains (respectively RNA) in protein-RNA interfaces from our dataset 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.本仓库包含与我们的研究论文《蛋白质-RNA同源界面的结构比较：普遍整体保守性与极性接触的多样性形成鲜明对比》相关的数据与代码。本研究中，我们通过构建蛋白质-RNA互作同源体（interolog，即同源界面）数据集，分析蛋白质-RNA界面的演化历程，探究同源界面间的界面接触保守性规律，并对非保守接触的成因展开探讨。 本仓库包含以下文件： DataAnalysisNotebook.ipynb：可复现本论文中接触保守性分析与全部图表的Jupyter交互式笔记本，同时支持数据探索工作。 env.yaml：用于构建运行该Jupyter笔记本所需的Conda/Mamba环境的配置文件。 2022-02-21-PDB.csv：包含蛋白质数据库（PDB）中含有相互作用蛋白与RNA链的复合物三维结构相关数据，具体字段包括PDB结构标识符、链标识符、实验技术与分辨率。 2022-02-21-PDB_proteinchainscontactingRNAchains.groupbp.tsv：包含上述复合物中相互作用蛋白与RNA链的更详细信息，具体包括PDB与链标识符、蛋白与RNA的分子大小、界面大小及接触数量。 2022-02-21-PDB_proteinchainscontactingRNAchains.groupbp.txt.selectXE_2.50_p30_r10_pi5_ri5_rep_bc-100.out_RNAcl_0.99.tsv：包含与上述文件一致的详细信息，但仅涵盖本研究互作同源体检索流程初始阶段所用的过滤后数据集。 PDBinterfaceAlign.csv：包含蛋白质-RNA相互作用对的结构比对相关信息，具体包括结构比对的TM评分（TM-score）、序列一致性与序列覆盖度。 DataInterologsParam.tsv：包含经预过滤的2587个潜在互作同源体的相关信息，具体包括界面均方根偏差（RMSD）、序列一致性、序列覆盖度及界面大小。 DataInterologsContactsFixedSASA.tsv：包含最终2022个互作同源体集合中保守与非保守接触的详细信息，具体包括氨基酸-核苷酸对的原子接触、非极性接触、氢键、盐桥与堆叠相互作用信息，以及各接触是否属于界面、所属二级结构，还有氨基酸表面可及性与演化保守性指标等内容。相较于V1版本，本文件修正了部分互作同源体对的溶剂可及性计算结果。 DataCons.csv：包含预计算的2022个互作同源体对的接触保守性指标，用于快速复现本论文的图表。 DataInterologsContactsResampledMaintainStructSeqId.tsv、DataInterologsContactsShuffled.tsv与DataInterologsShuffled.tsv：与接触保守性评估所用的基准计算结果相关。 clan.txt、clan_membership.txt、ecod.latest.domains.uniq.txt、rfam_interfaces_977.txt、DataGroupsECOD.tsv、DataGroupesRFAM.tsv、DataGroupsRFAMClan.tsv、DataInterfaceGroupsECOD.tsv与DataInterfaceGroupsRFAM.tsv：与本数据集蛋白质-RNA界面中蛋白质结构域（对应进化分类蛋白质结构域数据库ECOD）及RNA（对应RNA家族数据库Rfam）的分类信息相关。 ListeIntraHbonds.pkl与ListeIntraSaltBridges.pkl：为Pickle格式的数据文件，分别包含分子内氢键与盐桥信息，用于分析非保守极性接触的补偿机制。