{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T09:25:42Z","timestamp":1787995542794,"version":"build-2784847793"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Protein\u2013protein interactions are central to almost all biological functions, and the atomic details of such interactions can yield insights into the mechanisms that underlie these functions. We present a web server that wraps and extends the SwarmDock flexible protein\u2013protein docking algorithm. After uploading PDB files of the binding partners, the server generates low energy conformations and returns a ranked list of clustered docking poses and their corresponding structures. The user can perform full global docking, or focus on particular residues that are implicated in binding. The server is validated in the CAPRI blind docking experiment, against the most current docking benchmark, and against the ClusPro docking server, the highest performing server currently available.<\/jats:p>\n               <jats:p>Availability: The server is freely available and can be accessed at: http:\/\/bmm.cancerresearchuk.org\/%7ESwarmDock\/.<\/jats:p>\n               <jats:p>Contact: \u00a0Paul.Bates@cancer.org.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt038","type":"journal-article","created":{"date-parts":[[2013,1,24]],"date-time":"2013-01-24T01:45:41Z","timestamp":1358991941000},"page":"807-809","source":"Crossref","is-referenced-by-count":260,"title":["SwarmDock: a server for flexible protein\u2013protein docking"],"prefix":"10.1093","volume":"29","author":[{"given":"Mieczyslaw","family":"Torchala","sequence":"first","affiliation":[{"name":"1 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK and 2Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iain H.","family":"Moal","sequence":"additional","affiliation":[{"name":"1 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK and 2Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raphael A. G.","family":"Chaleil","sequence":"additional","affiliation":[{"name":"1 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK and 2Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Fernandez-Recio","sequence":"additional","affiliation":[{"name":"1 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK and 2Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul A.","family":"Bates","sequence":"additional","affiliation":[{"name":"1 Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK and 2Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, 08034 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,1,23]]},"reference":[{"key":"2023012810304276700_btt038-B1","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1093\/bioinformatics\/btg371","article-title":"ClusPro: an automated docking and discrimination method for the prediction of protein complexes","volume":"20","author":"Comeau","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012810304276700_btt038-B2","doi-asserted-by":"crossref","first-page":"3111","DOI":"10.1002\/prot.22830","article-title":"Protein-protein docking benchmark version 4.0","volume":"78","author":"Hwang","year":"2010","journal-title":"Proteins"},{"key":"2023012810304276700_btt038-B3","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1002\/prot.21804","article-title":"Docking and scoring protein complexes: CAPRI 3rd edition","volume":"69","author":"Lensink","year":"2007","journal-title":"Proteins"},{"key":"2023012810304276700_btt038-B4","doi-asserted-by":"crossref","first-page":"3189","DOI":"10.1002\/prot.22770","article-title":"Detection and refinement of encounter complexes for protein-protein docking: tacking account of macromolecular crowding","volume":"78","author":"Li","year":"2010","journal-title":"Proteins"},{"key":"2023012810304276700_btt038-B5","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1002\/prot.20019","article-title":"A physical reference state unifies the structure-derived potential of mean force for protein folding and binding","volume":"56","author":"Liu","year":"2004","journal-title":"Proteins"},{"key":"2023012810304276700_btt038-B6","doi-asserted-by":"crossref","first-page":"3623","DOI":"10.3390\/ijms11103623","article-title":"SwarmDock and the use of normal modes in protein-protein docking","volume":"11","author":"Moal","year":"2010","journal-title":"Int. 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