{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T11:34:45Z","timestamp":1780572885949,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009825","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,2,9]],"date-time":"2022-02-09T00:00:00Z","timestamp":1644364800000}}],"reference-count":80,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2022,1,28]],"date-time":"2022-01-28T00:00:00Z","timestamp":1643328000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Agence nationale de la recherche","award":["ANR-18-CE13-0004"],"award-info":[{"award-number":["ANR-18-CE13-0004"]}]},{"name":"Secr\u00e9tariat G\u00e9n\u00e9ral pour l\u2019Investissement","award":["ANR-11-BINF-0003 (MAPPING)"],"award-info":[{"award-number":["ANR-11-BINF-0003 (MAPPING)"]}]},{"name":"Secr\u00e9tariat g\u00e9n\u00e9ral pour l\u2019investissement","award":["ANR-10-EQPX- 29-01"],"award-info":[{"award-number":["ANR-10-EQPX- 29-01"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Proteins ensure their biological functions by interacting with each other. Hence, characterising protein interactions is fundamental for our understanding of the cellular machinery, and for improving medicine and bioengineering. Over the past years, a large body of experimental data has been accumulated on who interacts with whom and in what manner. However, these data are highly heterogeneous and sometimes contradictory, noisy, and biased.\n                    <jats:italic>Ab initio<\/jats:italic>\n                    methods provide a means to a \u201cblind\u201d protein-protein interaction network reconstruction. Here, we report on a molecular cross-docking-based approach for the identification of protein partners. The docking algorithm uses a coarse-grained representation of the protein structures and treats them as rigid bodies. We applied the approach to a few hundred of proteins, in the unbound conformations, and we systematically investigated the influence of several key ingredients, such as the size and quality of the interfaces, and the scoring function. We achieved some significant improvement compared to previous works, and a very high discriminative power on some specific functional classes. We provide a readout of the contributions of shape and physico-chemical complementarity, interface matching, and specificity, in the predictions. In addition, we assessed the ability of the approach to account for protein surface multiple usages, and we compared it with a sequence-based deep learning method. This work may contribute to guiding the exploitation of the large amounts of protein structural models now available toward the discovery of unexpected partners and their complex structure characterisation.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009825","type":"journal-article","created":{"date-parts":[[2022,1,28]],"date-time":"2022-01-28T13:38:23Z","timestamp":1643377103000},"page":"e1009825","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["From complete cross-docking to partners identification and binding sites predictions"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2864-5698","authenticated-orcid":true,"given":"Chlo\u00e9","family":"Dequeker","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0254-6595","authenticated-orcid":true,"given":"Yasser","family":"Mohseni Behbahani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"David","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4870-6304","authenticated-orcid":true,"given":"Elodie","family":"Laine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2098-5743","authenticated-orcid":true,"given":"Alessandra","family":"Carbone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,1,28]]},"reference":[{"key":"pcbi.1009825.ref001","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1142\/9789811211874_0005","article-title":"Mutational effects on protein\u2013protein interactions","author":"J Weako","year":"2020","journal-title":"Protein Interactions: Computational 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Ritchie","year":"2010","journal-title":"Bioinformatics"},{"issue":"6","key":"pcbi.1009825.ref042","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1110\/ps.0239303","article-title":"Protein-protein docking with a reduced protein model accounting for side-chain flexibility","volume":"12","author":"M Zacharias","year":"2003","journal-title":"Protein Sci"},{"key":"pcbi.1009825.ref043","first-page":"1","article-title":"Highly accurate protein structure prediction for the human proteome","author":"K Tunyasuvunakool","year":"2021","journal-title":"Nature"},{"key":"pcbi.1009825.ref044","article-title":"Protein interaction energy landscapes are shaped by functional and also non-functional partners","author":"H Schweke","year":"2020","journal-title":"Journal of Molecular Biology"},{"issue":"W1","key":"pcbi.1009825.ref045","doi-asserted-by":"crossref","first-page":"W417","DOI":"10.1093\/nar\/gky472","article-title":"Identification and visualization of protein binding regions with the ArDock server","volume":"46","author":"S Reille","year":"2018","journal-title":"Nucleic acids research"},{"issue":"10","key":"pcbi.1009825.ref046","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1002\/prot.25086","article-title":"Great interactions: How binding incorrect partners can teach us about protein recognition and function","volume":"84","author":"L Vamparys","year":"2016","journal-title":"Proteins"},{"issue":"1","key":"pcbi.1009825.ref047","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/2046-1682-5-7","article-title":"Arbitrary protein- protein docking targets biologically relevant interfaces","volume":"5","author":"J Martin","year":"2012","journal-title":"BMC biophysics"},{"issue":"3","key":"pcbi.1009825.ref048","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/j.jmb.2003.10.069","article-title":"Identification of Protein-Protein Interaction Sites From Docking Energy Landscapes","volume":"335","author":"J Fernandez-Recio","year":"2004","journal-title":"J Mol Biol"},{"issue":"3","key":"pcbi.1009825.ref049","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/(SICI)1097-0282(199609)39:3<455::AID-BIP16>3.0.CO;2-A","article-title":"Low-resolution docking: Prediction of complexes for underdetermined structures","volume":"39","author":"IA Vakser","year":"1996","journal-title":"Biopolymers"},{"issue":"1","key":"pcbi.1009825.ref050","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1002\/prot.25206","article-title":"Protein social behavior makes a stronger signal for partner identification than surface geometry","volume":"85","author":"E Laine","year":"2017","journal-title":"Proteins"},{"issue":"1","key":"pcbi.1009825.ref051","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s12859-017-1675-z","article-title":"Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks","volume":"18","author":"S Maheshwari","year":"2017","journal-title":"BMC bioinformatics"},{"key":"pcbi.1009825.ref052","doi-asserted-by":"crossref","unstructured":"Ohue M, Matsuzaki Y, Shimoda T, Ishida T, Akiyama Y. Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods. In: BMC proceedings. vol. 7. BioMed Central; 2013. p. S6.","DOI":"10.1186\/1753-6561-7-S7-S6"},{"issue":"12","key":"pcbi.1009825.ref053","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003369","article-title":"Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information","volume":"9","author":"A Lopes","year":"2013","journal-title":"PLoS computational biology"},{"key":"pcbi.1009825.ref054","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.jmb.2008.08.002","article-title":"Identification of protein interaction partners and protein-protein interaction sites","volume":"382","author":"S Sacquin-Mora","year":"2008","journal-title":"J Mol Biol"},{"issue":"Pt 6 No 1","key":"pcbi.1009825.ref055","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1107\/S0907444902003451","article-title":"The Protein Data Bank","volume":"58","author":"HM Berman","year":"2002","journal-title":"Acta Crystallogr D Biol 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Hashemifar","year":"2018","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1009825.ref062","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-017-08414-y","article-title":"Structure-based cross-docking analysis of antibody\u2013antigen interactions","volume":"7","author":"KP Kilambi","year":"2017","journal-title":"Scientific reports"},{"issue":"D1","key":"pcbi.1009825.ref063","doi-asserted-by":"crossref","first-page":"D465","DOI":"10.1093\/nar\/gkx1085","article-title":"Minimotif Miner 4: a million peptide minimotifs and counting","volume":"46","author":"KF Lyon","year":"2018","journal-title":"Nucleic acids research"},{"issue":"1","key":"pcbi.1009825.ref064","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/s13068-019-1436-5","article-title":"Peptide-based functional annotation of carbohydrate-active enzymes by conserved unique peptide patterns (CUPP)","volume":"12","author":"K Barrett","year":"2019","journal-title":"Biotechnology for 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