{"doi":"10.1101/2021.03.17.435706","title":"Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy","abstract":"Abstract Protein-protein interactions play a crucial role in almost all cellular processes. Identifying interacting proteins reveals insight into living organisms and yields novel drug targets for disease treatment. Here, we present a publicly available, automated pipeline to predict genome-wide protein-protein interactions and produce high-quality multimeric structural models. Application of our method to the Human and Yeast genomes yield protein-protein interaction networks similar in quality to common experimental methods. We identified and modeled Human proteins likely to interact with the papain-like protease of SARS-CoV2’s non-structural protein 3 (Nsp3). We also produced models of SARS-CoV2’s spike protein (S) interacting with myelin-oligodendrocyte glycoprotein receptor (MOG) and dipeptidyl peptidase-4 (DPP4). The presented method is capable of confidently identifying interactions while providing high-quality multimeric structural models for experimental validation. The interactome modeling pipeline is available at usegalaxy.org and usegalaxy.eu.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":223670,"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":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9408,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":478954,"name":"Dannon Baker","orcid":"0000-0002-4882-5357","position":1,"is_corresponding":false},{"id":11439,"name":"Marius van den Beek","orcid":"0000-0002-9676-7032","position":2,"is_corresponding":false},{"id":825900,"name":"Bjoern Gruening","orcid":null,"position":3,"is_corresponding":false},{"id":478955,"name":"Dave Bouvier","orcid":"0000-0001-8031-5069","position":4,"is_corresponding":false},{"id":480025,"name":"Nate Coraor","orcid":null,"position":5,"is_corresponding":false},{"id":23978,"name":"Stephen D. Shank","orcid":"0000-0003-0734-9953","position":6,"is_corresponding":false},{"id":813448,"name":"Jordan D. Zehr","orcid":"0000-0003-2099-4172","position":7,"is_corresponding":false},{"id":24539,"name":"Michael C. Schatz","orcid":"0000-0002-4118-4446","position":8,"is_corresponding":false},{"id":19433,"name":"Anton Nekrutenko","orcid":"0000-0002-5987-8032","position":9,"is_corresponding":false},{"id":77458,"name":"Aysam Guerler","orcid":"0000-0001-6513-2539","position":0,"is_corresponding":true}],"reference_count":51,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:54:14.760456Z","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":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}