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Here, the ABSINTH implicit solvent model and force field are extended to describe small, organic molecules and their interactions with proteins. We show that an automatic pipeline based on partitioning arbitrary molecules into substructures corresponding to model compounds with known free energies of solvation can be combined with the CHARMM general force field into a method that is successful at the two important challenges a scoring function faces in virtual screening work flows: it ranks known binders with correlation values rivaling that of comparable state-of-the-art methods and it enriches true binders in a set of decoys. Our protocol introduces innovative modifications to common virtual screening workflows, notably the use of explicit ions as competitors and the integration over multiple protein and ligand species differing in their protonation states. We demonstrate the value of modifications to both the protocol and ABSINTH itself. We conclude by discussing the limitations of high-throughput implicit methods such as the one proposed here.<\/jats:p>","DOI":"10.1021\/acs.jcim.0c00558","type":"journal-article","created":{"date-parts":[[2020,9,8]],"date-time":"2020-09-08T11:39:58Z","timestamp":1599565198000},"page":"5188-5202","source":"Crossref","is-referenced-by-count":13,"title":["An ABSINTH-Based Protocol for Predicting Binding Affinities\nbetween Proteins and Small Molecules"],"prefix":"10.1021","volume":"60","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8002-9457","authenticated-orcid":true,"given":"Jean-Re\u0301my","family":"Marchand","sequence":"first","affiliation":[{"name":"University of Zu\u0308rich , , ,","place":["Zu\u0308rich, Switzerland, CH 8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim","family":"Knehans","sequence":"additional","affiliation":[{"name":"University of Zu\u0308rich , , ,","place":["Zu\u0308rich, Switzerland, CH 8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2317-6792","authenticated-orcid":true,"given":"Amedeo","family":"Caflisch","sequence":"additional","affiliation":[{"name":"University of Zu\u0308rich , , ,","place":["Zu\u0308rich, Switzerland, CH 8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5422-5278","authenticated-orcid":true,"given":"Andreas","family":"Vitalis","sequence":"additional","affiliation":[{"name":"University of Zu\u0308rich , , ,","place":["Zu\u0308rich, Switzerland, CH 8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,9,8]]},"reference":[{"key":"2026081804380578100_cit1","doi-asserted-by":"publisher","first-page":"D1083","DOI":"10.1093\/nar\/gkt1031","article-title":"The ChEMBL\nbioactivity database:\nan update","volume":"42","author":"Bento","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2026081804380578100_cit2","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1111\/j.1476-5381.2010.01127.x","article-title":"Principles of early\ndrug discovery","volume":"162","author":"Hughes","year":"2011","journal-title":"Br. 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