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By using a combination of simple structural properties, such as the residue-contacts made at the interface, PRODIGY has demonstrated a top performance compared with other state-of-the-art predictors in the literature. Here we present an extension of it, named PRODIGY-LIG, aimed at the prediction of affinity in protein-small ligand complexes. The predictive method, properly readapted for small ligand by making use of atomic instead of residue contacts, has been successfully applied for the blind prediction of 102 protein\u2013ligand complexes during the D3R Grand Challenge 2. PRODIGY-LIG has the advantage of being simple, generic and applicable to any kind of protein-ligand complex. It provides an automatic, fast and user-friendly tool ensuring broad accessibility.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>PRODIGY-LIG is freely available without registration requirements at http:\/\/milou.science.uu.nl\/services\/PRODIGY-LIG.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty816","type":"journal-article","created":{"date-parts":[[2018,9,19]],"date-time":"2018-09-19T20:32:35Z","timestamp":1537389155000},"page":"1585-1587","source":"Crossref","is-referenced-by-count":236,"title":["Large-scale prediction of binding affinity in protein\u2013small ligand complexes: the PRODIGY-LIG web server"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2485-7378","authenticated-orcid":false,"given":"Anna","family":"Vangone","sequence":"first","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4389-2366","authenticated-orcid":false,"given":"Joerg","family":"Schaarschmidt","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Panagiotis","family":"Koukos","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cunliang","family":"Geng","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nevia","family":"Citro","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikael E","family":"Trellet","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li C","family":"Xue","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7369-1322","authenticated-orcid":false,"given":"Alexandre M J J","family":"Bonvin","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,9,20]]},"reference":[{"key":"2023012806491456700_bty816-B1","doi-asserted-by":"crossref","first-page":"baw007","DOI":"10.1093\/database\/baw007","article-title":"2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions","volume":"2016","author":"Basse","year":"2016","journal-title":"Database (Oxford)"},{"key":"2023012806491456700_bty816-B2","doi-asserted-by":"crossref","first-page":"3097","DOI":"10.1021\/ci400510e","article-title":"Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction","volume":"53","author":"Brylinski","year":"2013","journal-title":"J. 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