{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:51:23Z","timestamp":1767963083465,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Protein\u2013protein interactions play a critical role in many biological processes. Despite that, the number of servers that provide an easy and comprehensive method to predict them is still limited. Here, we present iLoops, a web server that predicts whether a pair of proteins can interact using local structural features. The inputs of the server are as follows: (i) the sequences of the query proteins and (ii) the pairs to be tested. Structural features are assigned to the query proteins by sequence similarity. Pairs of structural features (formed by loops or domains) are classified according to their likelihood to favor or disfavor a protein\u2013protein interaction, depending on their observation in known interacting and non-interacting pairs. The server evaluates the putative interaction using a random forest classifier.<\/jats:p>\n               <jats:p>Availability: iLoops is available at http:\/\/sbi.imim.es\/iLoops.php<\/jats:p>\n               <jats:p>Contact: \u00a0baldo.oliva@upf.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt401","type":"journal-article","created":{"date-parts":[[2013,7,11]],"date-time":"2013-07-11T00:34:28Z","timestamp":1373502868000},"page":"2360-2362","source":"Crossref","is-referenced-by-count":46,"title":["iLoops: a protein\u2013protein interaction prediction server based on structural features"],"prefix":"10.1093","volume":"29","author":[{"given":"Joan","family":"Planas-Iglesias","sequence":"first","affiliation":[{"name":"Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuel A.","family":"Marin-Lopez","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaume","family":"Bonet","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javier","family":"Garcia-Garcia","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Baldo","family":"Oliva","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,7,9]]},"reference":[{"key":"2023070311400614200_btt401-B1","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1093\/bioinformatics\/19.1.161","article-title":"InterPreTS: protein interaction prediction through tertiary structure","volume":"19","author":"Aloy","year":"2003","journal-title":"Bioinformatics"},{"key":"2023070311400614200_btt401-B2","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023070311400614200_btt401-B3","doi-asserted-by":"crossref","first-page":"D419","DOI":"10.1093\/nar\/gkm993","article-title":"Data growth and its impact on the SCOP database: new developments","volume":"36","author":"Andreeva","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023070311400614200_btt401-B4","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-7-S1-S2","article-title":"Choosing negative examples for the prediction of protein-protein interactions","volume":"7","author":"Ben-Hur","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023070311400614200_btt401-B5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nmeth.1281","article-title":"An experimentally derived confidence score for binary protein-protein interactions","volume":"6","author":"Braun","year":"2009","journal-title":"Nat. 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