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The server takes as input either several sequences or 3D structures of proteins known to interact. It returns a set of 10 consensus candidate complexes, together with interface predictions to guide further experimental validation interactively. Three key novelties were implemented in InterEvDock3 to help obtain more reliable models: users can (i) generate template-based structural models of assemblies using close and remote homologs of known 3D structure, detected through an automated search protocol, (ii) select the assembly models most consistent with contact maps from external methods that implement covariation-based contact prediction with or without deep learning and (iii) exploit a novel coevolution-based scoring scheme at atomic level, which leads to significantly higher free docking success rates. The performance of the server was validated on two large free docking benchmark databases, containing respectively 230 unbound targets (Weng dataset) and 812 models of unbound targets (PPI4DOCK dataset). Its effectiveness has also been proven on a number of challenging examples. The InterEvDock3 web interface is available at http:\/\/bioserv.rpbs.univ-paris-diderot.fr\/services\/InterEvDock3\/.<\/jats:p>","DOI":"10.1093\/nar\/gkab358","type":"journal-article","created":{"date-parts":[[2021,4,23]],"date-time":"2021-04-23T11:12:28Z","timestamp":1619176348000},"page":"W277-W284","source":"Crossref","is-referenced-by-count":30,"title":["InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps"],"prefix":"10.1093","volume":"49","author":[{"given":"Chlo\u00e9","family":"Quignot","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198\u00a0Gif-sur-Yvette, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guillaume","family":"Postic","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS UMR 8251, INSERM U1133, RPBS, Paris 75205, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H\u00e9l\u00e8ne","family":"Bret","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198\u00a0Gif-sur-Yvette, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julien","family":"Rey","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS UMR 8251, INSERM U1133, RPBS, Paris 75205, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre","family":"Granger","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198\u00a0Gif-sur-Yvette, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel","family":"Murail","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS UMR 8251, INSERM U1133, RPBS, Paris 75205, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3168-4826","authenticated-orcid":false,"given":"Pablo","family":"Chac\u00f3n","sequence":"additional","affiliation":[{"name":"Department of Biological Physical Chemistry, Rocasolano Institute of Physical Chemistry C.S.I.C, Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4435-9093","authenticated-orcid":false,"given":"Jessica","family":"Andreani","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198\u00a0Gif-sur-Yvette, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1033-9895","authenticated-orcid":false,"given":"Pierre","family":"Tuff\u00e9ry","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, CNRS UMR 8251, INSERM U1133, RPBS, Paris 75205, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5294-2858","authenticated-orcid":false,"given":"Rapha\u00ebl","family":"Guerois","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198\u00a0Gif-sur-Yvette, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,5,12]]},"reference":[{"key":"2021070812070376800_B1","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1146\/annurev-biochem-060614-034142","article-title":"Structure, dynamics, assembly, and evolution of protein complexes","volume":"84","author":"Marsh","year":"2015","journal-title":"Annu. 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