{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,10]],"date-time":"2026-06-10T04:48:33Z","timestamp":1781066913705,"version":"3.54.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,11,10]],"date-time":"2016-11-10T00:00:00Z","timestamp":1478736000000},"content-version":"vor","delay-in-days":911,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,1]]},"DOI":"10.1093\/nar\/gku397","type":"journal-article","created":{"date-parts":[[2014,5,15]],"date-time":"2014-05-15T05:40:44Z","timestamp":1400132444000},"page":"W285-W289","source":"Crossref","is-referenced-by-count":192,"title":["PRISM: a web server and repository for prediction of protein\u2013protein interactions and modeling their 3D complexes"],"prefix":"10.1093","volume":"42","author":[{"given":"Alper","family":"Baspinar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Engin","family":"Cukuroglu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Nussinov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ozlem","family":"Keskin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Attila","family":"Gursoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,5,14]]},"reference":[{"key":"key\n\t\t\t\t20171011202751_B1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/nmeth.1280","article-title":"An empirical framework for binary interactome mapping","volume":"6","author":"Venkatesan","year":"2009","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20171011202751_B2","doi-asserted-by":"crossref","first-page":"6959","DOI":"10.1073\/pnas.0708078105","article-title":"Estimating the size of the human interactome","volume":"105","author":"Stumpf","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"key\n\t\t\t\t20171011202751_B3","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nmeth.2289","article-title":"Interactome3D: adding structural details to protein networks","volume":"10","author":"Mosca","year":"2013","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20171011202751_B4","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1038\/embor.2011.261","article-title":"Large-scale mapping of human protein interactome using structural complexes","volume":"13","author":"Tyagi","year":"2012","journal-title":"EMBO Rep."},{"key":"key\n\t\t\t\t20171011202751_B5","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.sbi.2012.04.004","article-title":"Constructing structural networks of signaling pathways on the proteome scale","volume":"22","author":"Kuzu","year":"2012","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20171011202751_B6","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1016\/j.str.2011.04.006","article-title":"Protein-protein complex structure predictions by multimeric threading and template recombination","volume":"19","author":"Mukherjee","year":"2011","journal-title":"Structure"},{"key":"key\n\t\t\t\t20171011202751_B7","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1021\/ci300579r","article-title":"Mapping monomeric threading to protein-protein structure prediction","volume":"53","author":"Guerler","year":"2013","journal-title":"J. Chem. Inf. Model."},{"key":"key\n\t\t\t\t20171011202751_B8","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1002\/prot.10222","article-title":"MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading","volume":"49","author":"Lu","year":"2002","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171011202751_B9","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1038\/nprot.2011.367","article-title":"Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM","volume":"6","author":"Tuncbag","year":"2011","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t20171011202751_B10","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1002\/prot.24022","article-title":"Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement","volume":"80","author":"Tuncbag","year":"2012","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171011202751_B11","doi-asserted-by":"crossref","first-page":"2641","DOI":"10.1021\/pr400006k","article-title":"Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale","volume":"12","author":"Kuzu","year":"2013","journal-title":"J. Proteome Res."},{"key":"key\n\t\t\t\t20171011202751_B12","doi-asserted-by":"crossref","first-page":"2137","DOI":"10.1002\/prot.24392","article-title":"Global and local structural similarity in protein-protein complexes: implications for template-based docking","volume":"81","author":"Kundrotas","year":"2013","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171011202751_B13","doi-asserted-by":"crossref","first-page":"2850","DOI":"10.1093\/bioinformatics\/bti443","article-title":"Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces","volume":"21","author":"Aytuna","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011202751_B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/jmbi.1998.1843","article-title":"Anatomy of hot spots in protein interfaces","volume":"280","author":"Bogan","year":"1998","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171011202751_B15","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1126\/science.7529940","article-title":"A hot spot of binding energy in a hormone-receptor interface","volume":"267","author":"Clackson","year":"1995","journal-title":"Science"},{"key":"key\n\t\t\t\t20171011202751_B16","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011202751_B17","doi-asserted-by":"crossref","first-page":"W331","DOI":"10.1093\/nar\/gki585","article-title":"PRISM: protein interactions by structural matching","volume":"33","author":"Ogmen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011202751_B18","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1002\/prot.22668","article-title":"FiberDock: flexible induced-fit backbone refinement in molecular docking","volume":"78","author":"Mashiach","year":"2010","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171011202751_B19","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/jp973084f","article-title":"All-atom empirical potential for molecular modeling and dynamics studies of proteins","volume":"102","author":"MacKerell","year":"1998","journal-title":"J. Phys. Chem. B"},{"key":"key\n\t\t\t\t20171011202751_B20","doi-asserted-by":"crossref","first-page":"e86738","DOI":"10.1371\/journal.pone.0086738","article-title":"Non-redundant unique interface structures as templates for modeling protein interactions","volume":"9","author":"Cukuroglu","year":"2014","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20171011202751_B21","doi-asserted-by":"crossref","first-page":"D829","DOI":"10.1093\/nar\/gkr929","article-title":"HotRegion: a database of predicted hot spot clusters","volume":"40","author":"Cukuroglu","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011202751_B22","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1093\/bioinformatics\/btp240","article-title":"Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy","volume":"25","author":"Tuncbag","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011202751_B23","article-title":"'NACCESS', Computer Program","author":"Hubbard","year":"1993"},{"key":"key\n\t\t\t\t20171011202751_B24","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1002\/prot.10628","article-title":"A method for simultaneous alignment of multiple protein structures","volume":"56","author":"Shatsky","year":"2004","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171011202751_B25","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1002\/ijch.201300024","article-title":"JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia","volume":"53","author":"Hanson","year":"2013","journal-title":"Isr. J. Chem."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/42\/W1\/W285\/7444745\/gku397.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,19]],"date-time":"2020-08-19T12:31:47Z","timestamp":1597840307000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/42\/W1\/W285\/2437127\/PRISM-a-web-server-and-repository-for-prediction"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,5,14]]},"references-count":25,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2014,5,14]]},"published-print":{"date-parts":[[2014,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gku397","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,7,1]]},"published":{"date-parts":[[2014,5,14]]}}}