{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T18:07:14Z","timestamp":1776794834456,"version":"3.51.2"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2017,2,14]],"date-time":"2017-02-14T00:00:00Z","timestamp":1487030400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM116960"],"award-info":[{"award-number":["R01 GM116960"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["FC001003"],"award-info":[{"award-number":["FC001003"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003141","name":"Consejo Nacional de Ciencia y Tecnolog\u00eda","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003141","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Atomic modeling of protein\u2013protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>IRaPPA has been implemented in the SwarmDock server (http:\/\/bmm.crick.ac.uk\/\u223cSwarmDock\/), pyDock server (http:\/\/life.bsc.es\/pid\/pydockrescoring\/) and ZDOCK server (http:\/\/zdock.umassmed.edu\/), with code available on request.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx068","type":"journal-article","created":{"date-parts":[[2017,2,15]],"date-time":"2017-02-15T08:58:08Z","timestamp":1487149088000},"page":"1806-1813","source":"Crossref","is-referenced-by-count":39,"title":["IRaPPA: information retrieval based integration of biophysical models for protein assembly selection"],"prefix":"10.1093","volume":"33","author":[{"given":"Iain H","family":"Moal","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"},{"name":"Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Didier","family":"Barradas-Bautista","sequence":"additional","affiliation":[{"name":"Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian","family":"Jim\u00e9nez-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mieczyslaw","family":"Torchala","sequence":"additional","affiliation":[{"name":"Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arjan","family":"van der Velde","sequence":"additional","affiliation":[{"name":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"},{"name":"Bioinformatics Program, Boston University, Boston, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thom","family":"Vreven","sequence":"additional","affiliation":[{"name":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiping","family":"Weng","sequence":"additional","affiliation":[{"name":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul A","family":"Bates","sequence":"additional","affiliation":[{"name":"Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan","family":"Fern\u00e1ndez-Recio","sequence":"additional","affiliation":[{"name":"Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,2,14]]},"reference":[{"key":"2023020205313789600_btx068-B1","doi-asserted-by":"crossref","first-page":"e0161879.","DOI":"10.1371\/journal.pone.0161879","article-title":"DockQ: a quality measure for protein\u2013protein docking models","volume":"11","author":"Basu","year":"2016","journal-title":"PLoS ONE"},{"key":"2023020205313789600_btx068-B2","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1007\/BF00058655","article-title":"Bagging predictors","volume":"24","author":"Breiman","year":"1996","journal-title":"Mach. 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