{"doi":"10.7554/elife.100485","title":"Establishing comprehensive quaternary structural proteomes from genome sequence","abstract":"Abstract A critical body of knowledge has developed through advances in protein microscopy, protein-fold modeling, structural biology software, availability of sequenced bacterial genomes, large-scale mutation databases, and genome-scale models. Based on these recent advances, we develop a computational framework that; i) identifies the oligomeric structural proteome encoded by an organism’s genome from available structural resources; ii) maps multi-strain alleleomic variation, resulting in the structural proteome for a species; and iii) calculates the 3D orientation of proteins across subcellular compartments with residue-level precision. Using the platform, we; iv) compute the quaternary E. coli K-12 MG1655 structural proteome; v) use a dataset of 12,000 mutations to build Random Forest classifiers that can predict the severity of mutations; and, in combination with a genome-scale model that computes proteome allocation, vi) obtain the spatial allocation of the E. coli proteome. Thus, in conjunction with relevant datasets and increasingly accurate computational models, we can now annotate quaternary structural proteomes, at genome-scale, to obtain a molecular-level understanding of whole-cell functions.","journal":"eLife","year":2024,"id":503742,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10062,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8548,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":60.4167,"fair_percentile":80.03668602873739,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":5431,"name":"Nathan Mih","orcid":"0000-0002-4302-9052","position":1,"is_corresponding":false},{"id":1172281,"name":"Maxwell Lu","orcid":null,"position":2,"is_corresponding":false},{"id":5441,"name":"Bernhard Ø. Palsson","orcid":"0000-0003-2357-6785","position":3,"is_corresponding":false},{"id":988639,"name":"Edward Catoiu","orcid":"0000-0001-8680-7291","position":0,"is_corresponding":true}],"reference_count":63,"raw_metadata":null,"created_at":"2026-07-19T02:10:31.826282Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":38.8889,"fair_a":81.25,"fair_i":60.0,"fair_r":45.8333,"fair_zscore":1.0278,"fair_rationale":{"fair_score":60.42,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":38.89,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Data generated in this study is provided in the Supplementary Material and/or at https://github.com /EdwardCatoiu/QSPACE/ .","grounded":true,"rationale":"The only identifier for the data is a web URL (GitHub), not a persistent identifier scheme. 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