{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T09:04:07Z","timestamp":1776416647474,"version":"3.51.2"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"23","funder":[{"name":"Marie Sk\u0142odowska-Curie Individual Fellowship","award":["H2020 MSCA-IF-2015"],"award-info":[{"award-number":["H2020 MSCA-IF-2015"]}]},{"name":"Marie Sk\u0142odowska-Curie Individual Fellowship","award":["BAP-659025"],"award-info":[{"award-number":["BAP-659025"]}]},{"DOI":"10.13039\/501100003246","name":"Netherlands Organisation for Scientific Research","doi-asserted-by":"crossref","award":["722.014.005"],"award-info":[{"award-number":["722.014.005"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,1]]},"abstract":"<jats:p>Summary: Gaining insights into the structural determinants of protein\u2013protein interactions holds the key for a deeper understanding of biological functions, diseases and development of therapeutics. An important aspect of this is the ability to accurately predict the binding strength for a given protein\u2013protein complex. Here we present PROtein binDIng enerGY prediction (PRODIGY), a web server to predict the binding affinity of protein\u2013protein complexes from their 3D structure. The PRODIGY server implements our simple but highly effective predictive model based on intermolecular contacts and properties derived from non-interface surface.<\/jats:p>\n               <jats:p>Availability and Implementation: PRODIGY is freely available at: http:\/\/milou.science.uu.nl\/services\/PRODIGY.<\/jats:p>\n               <jats:p>Contact: \u00a0a.m.j.j.bonvin@uu.nl, a.vangone@uu.nl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw514","type":"journal-article","created":{"date-parts":[[2016,8,9]],"date-time":"2016-08-09T01:43:59Z","timestamp":1470707039000},"page":"3676-3678","source":"Crossref","is-referenced-by-count":1217,"title":["PRODIGY: a web server for predicting the binding affinity of protein\u2013protein complexes"],"prefix":"10.1093","volume":"32","author":[{"given":"Li C.","family":"Xue","sequence":"first","affiliation":[]},{"given":"Jo\u00e3o Pglm","family":"Rodrigues","sequence":"additional","affiliation":[]},{"given":"Panagiotis L.","family":"Kastritis","sequence":"additional","affiliation":[]},{"given":"Alexandre Mjj","family":"Bonvin","sequence":"additional","affiliation":[]},{"given":"Anna","family":"Vangone","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2016,8,8]]},"reference":[{"key":"2023020114090534000_btw514-B1","doi-asserted-by":"crossref","DOI":"10.1038\/256705a0","article-title":"Principles of protein\u2013protein recognition","author":"Chothia","year":"1975","journal-title":"Nature"},{"key":"2023020114090534000_btw514-B2","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1002\/pro.5560010117","article-title":"Calculation of the free energy of association for protein complexes","volume":"1","author":"Horton","year":"1992","journal-title":"Protein Sci"},{"key":"2023020114090534000_btw514-B3","author":"Hubbard","year":"1993"},{"key":"2023020114090534000_btw514-B4","doi-asserted-by":"crossref","first-page":"2216","DOI":"10.1021\/pr9009854","article-title":"Are scoring functions in protein\u2212protein docking ready to predict interactomes? 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