{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T07:44:58Z","timestamp":1762674298568,"version":"3.37.3"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Interpretation of ubiquitous protein sequence data has become a bottleneck in biomolecular research, due to a lack of structural and other experimental annotation data for these proteins. Prediction of protein interaction sites from sequence may be a viable substitute. We therefore recently developed a sequence-based random forest method for protein\u2013protein interface prediction, which yielded a significantly increased performance than other methods on both homomeric and heteromeric protein\u2013protein interactions. Here, we present a webserver that implements this method efficiently.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>With the aim of accelerating our previous approach, we obtained sequence conservation profiles by re-mastering the alignment of homologous sequences found by PSI-BLAST. This yielded a more than 10-fold speedup and at least the same accuracy, as reported previously for our method; these results allowed us to offer the method as a webserver. The web-server interface is targeted to the non-expert user. The input is simply a sequence of the protein of interest, and the output a table with scores indicating the likelihood of having an interaction interface at a certain position. As the method is sequence-based and not sensitive to the type of protein interaction, we expect this webserver to be of interest to many biological researchers in academia and in industry.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Webserver, source code and datasets are available at www.ibi.vu.nl\/programs\/serendipwww\/.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz428","type":"journal-article","created":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T19:15:04Z","timestamp":1558120504000},"page":"4794-4796","source":"Crossref","is-referenced-by-count":22,"title":["SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions"],"prefix":"10.1093","volume":"35","author":[{"given":"Qingzhen","family":"Hou","sequence":"first","affiliation":[{"name":"Department of BioModeling, BioInformatics & BioProcesses, Universit\u00e9 Libre de Bruxelles , Brussels 1050, Belgium"}]},{"given":"Paul F G","family":"De Geest","sequence":"additional","affiliation":[{"name":"IBIVU \u2013 Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam , Amsterdam 1081HV, The Netherlands"}]},{"given":"Christian J","family":"Griffioen","sequence":"additional","affiliation":[{"name":"IBIVU \u2013 Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam , Amsterdam 1081HV, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2779-7174","authenticated-orcid":false,"given":"Sanne","family":"Abeln","sequence":"additional","affiliation":[{"name":"IBIVU \u2013 Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam , Amsterdam 1081HV, The Netherlands"}]},{"given":"Jaap","family":"Heringa","sequence":"additional","affiliation":[{"name":"IBIVU \u2013 Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam , Amsterdam 1081HV, The Netherlands"},{"name":"AIMMS \u2013 Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam , Amsterdam 1081HV, The Netherlands"}]},{"given":"K Anton","family":"Feenstra","sequence":"additional","affiliation":[{"name":"IBIVU \u2013 Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam , Amsterdam 1081HV, The Netherlands"},{"name":"AIMMS \u2013 Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam , Amsterdam 1081HV, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2023013108354242400_btz428-B1","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1186\/s12859-015-0758-y","article-title":"Sequence specificity between interacting and non-interacting homologs identifies interface residues \u2013 a homodimer and monomer use case","volume":"16","author":"Hou","year":"2015","journal-title":"BMC bioinformatics"},{"key":"2023013108354242400_btz428-B2","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1093\/bioinformatics\/btx005","article-title":"Seeing the trees through the forest: sequence-based homo and heteromeric protein-protein interaction sites prediction using random forest","volume":"33","author":"Hou","year":"2017","journal-title":"Bioinformatics"},{"key":"2023013108354242400_btz428-B3","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1016\/j.str.2013.08.007","article-title":"Protein modeling: what happened to the \u201cprotein structure gap\u201d?","volume":"21","author":"Schwede","year":"2013","journal-title":"Structure"},{"key":"2023013108354242400_btz428-B4","doi-asserted-by":"crossref","first-page":"e42","DOI":"10.1371\/journal.pcbi.0030042","article-title":"Deciphering protein-protein interactions. Part I. Experimental techniques and databases","volume":"3","author":"Shoemaker","year":"2007","journal-title":"PLoS Comput. Biol"},{"key":"2023013108354242400_btz428-B5","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/j.compbiolchem.2004.09.005","article-title":"The influence of gapped positions in multiple sequence alignments on secondary structure prediction methods","volume":"28","author":"Simossis","year":"2004","journal-title":"Comput. Biol. Chem"},{"key":"2023013108354242400_btz428-B6","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1093\/bib\/bbp001","article-title":"A survey of available tools and web servers for analysis of protein-protein interactions and interfaces","volume":"10","author":"Tuncbag","year":"2008","journal-title":"Brief. Bioinformatics"},{"key":"2023013108354242400_btz428-B7","doi-asserted-by":"crossref","first-page":"11503","DOI":"10.1073\/pnas.0600489103","article-title":"Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease","author":"Wang","year":"2006","journal-title":"Proceedings of the National Academy of Sciences"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz428\/28875322\/btz428.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/22\/4794\/48978343\/bioinformatics_35_22_4794.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/22\/4794\/48978343\/bioinformatics_35_22_4794.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,16]],"date-time":"2023-09-16T18:04:55Z","timestamp":1694887495000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/22\/4794\/5497259"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,5,22]]},"references-count":7,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz428","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,11,15]]},"published":{"date-parts":[[2019,5,22]]}}}