{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:52Z","timestamp":1772138092080,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2018,11,6]],"date-time":"2018-11-06T00:00:00Z","timestamp":1541462400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Prediction and identification of key determinants of protein-protein interaction specificity"},{"name":"Dutch Graduate School Experimental Plant Sciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Predicting residue\u2013residue contacts between interacting proteins is an important problem in bioinformatics. The growing wealth of sequence data can be used to infer these contacts through correlated mutation analysis on multiple sequence alignments of interacting homologs of the proteins of interest. This requires correct identification of pairs of interacting proteins for many species, in order to avoid introducing noise (i.e. non-interacting sequences) in the analysis that will decrease predictive performance.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We have designed Ouroboros, a novel algorithm to reduce such noise in intermolecular contact prediction. Our method iterates between weighting proteins according to how likely they are to interact based on the correlated mutations signal, and predicting correlated mutations based on the weighted sequence alignment. We show that this approach accurately discriminates between protein interaction versus non-interaction and simultaneously improves the prediction of intermolecular contact residues compared to a naive application of correlated mutation analysis. This requires no training labels concerning interactions or contacts. Furthermore, the method relaxes the assumption of one-to-one interaction of previous approaches, allowing for the study of many-to-many interactions.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n Source code and test data are available at www.bif.wur.nl\/.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty924","type":"journal-article","created":{"date-parts":[[2018,11,5]],"date-time":"2018-11-05T15:13:13Z","timestamp":1541430793000},"page":"2036-2042","source":"Crossref","is-referenced-by-count":7,"title":["Improved inference of intermolecular contacts through protein\u2013protein interaction prediction using coevolutionary analysis"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3840-3273","authenticated-orcid":false,"given":"Miguel","family":"Correa Marrero","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Plant Sciences"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0182-4138","authenticated-orcid":false,"given":"Richard G H","family":"Immink","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology, Department of Plant Sciences"},{"name":"Bioscience, Wageningen Plant Research"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4944-4310","authenticated-orcid":false,"given":"Dick","family":"de Ridder","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Plant Sciences"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8872-5123","authenticated-orcid":false,"given":"Aalt D J","family":"van Dijk","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Plant Sciences"},{"name":"Bioscience, Wageningen Plant Research"},{"name":"Biometris, Department of Plant Sciences, Wageningen University & Research, Wageningen PB, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2018,11,6]]},"reference":[{"key":"2023012713073436000_bty924-B1","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.abb.2014.05.010","article-title":"Evolution of protein interactions: from interactomes to interfaces","volume":"554","author":"Andreani","year":"2014","journal-title":"Arch. 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