{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:41Z","timestamp":1772138081142,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>Motivation: Protein\u2013protein docking methods are of great importance for understanding interactomes at the structural level. It has become increasingly appealing to use not only experimental structures but also homology models of unbound subunits as input for docking simulations. So far we are missing a large scale assessment of the success of rigid-body free docking methods on homology models.<\/jats:p>\n                  <jats:p>Results: We explored how we could benefit from comparative modelling of unbound subunits to expand docking benchmark datasets. Starting from a collection of 3157 non-redundant, high X-ray resolution heterodimers, we developed the PPI4DOCK benchmark containing 1417 docking targets based on unbound homology models. Rigid-body docking by Zdock showed that for 1208 cases (85.2%), at least one correct decoy was generated, emphasizing the efficiency of rigid-body docking in generating correct assemblies. Overall, the PPI4DOCK benchmark contains a large set of realistic cases and provides new ground for assessing docking and scoring methodologies.<\/jats:p>\n                  <jats:p>Availability and Implementation: Benchmark sets can be downloaded from http:\/\/biodev.cea.fr\/interevol\/ppi4dock\/<\/jats:p>\n                  <jats:p>Contact: \u00a0guerois@cea.fr<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw533","type":"journal-article","created":{"date-parts":[[2016,8,22]],"date-time":"2016-08-22T20:28:57Z","timestamp":1471897737000},"page":"3760-3767","source":"Crossref","is-referenced-by-count":35,"title":["PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets"],"prefix":"10.1093","volume":"32","author":[{"given":"Jinchao","family":"Yu","sequence":"first","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Univ Paris-Sud, Universit\u00e9 Paris-Saclay, F-91198, Gif-sur-Yvette, France"}]},{"given":"Rapha\u00ebl","family":"Guerois","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Univ Paris-Sud, Universit\u00e9 Paris-Saclay, F-91198, Gif-sur-Yvette, France"}]}],"member":"286","published-online":{"date-parts":[[2016,8,22]]},"reference":[{"key":"2023020114090987300_btw533-B1","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1093\/bioinformatics\/18.1.175","article-title":"SACS\u2013self-maintaining database of antibody crystal structure information","volume":"18","author":"Allcorn","year":"2002","journal-title":"Bioinformatics"},{"key":"2023020114090987300_btw533-B2","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1002\/prot.24385","article-title":"Protein models: the grand challenge of protein docking","volume":"82","author":"Anishchenko","year":"2014","journal-title":"Proteins"},{"key":"2023020114090987300_btw533-B3","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1002\/prot.24784","article-title":"Protein models docking benchmark 2","volume":"83","author":"Anishchenko","year":"2015","journal-title":"Proteins"},{"key":"2023020114090987300_btw533-B4","first-page":"1","article-title":"A benchmark testing ground for integrating homology modeling and protein docking","author":"Bohnuud","year":"2016","journal-title":"Proteins"},{"key":"2023020114090987300_btw533-B5","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: a hub for protein information","volume":"43","author":"Consortium","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020114090987300_btw533-B6","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1038\/nprot.2010.32","article-title":"The HADDOCK web server for data-driven biomolecular docking","volume":"5","author":"de Vries","year":"2010","journal-title":"Nat. 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