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From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms.<\/jats:p><jats:p>Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects.<\/jats:p><jats:p>Availability and Implementation: \u00a0http:\/\/adfr.scripps.edu\/AutoDockFR\/autosite.html<\/jats:p><jats:p>Contact: \u00a0sanner@scripps.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw367","type":"journal-article","created":{"date-parts":[[2016,6,29]],"date-time":"2016-06-29T14:57:42Z","timestamp":1467212262000},"page":"3142-3149","source":"Crossref","is-referenced-by-count":100,"title":["AutoSite: an automated approach for pseudo-ligands prediction\u2014from ligand-binding sites identification to predicting key ligand atoms"],"prefix":"10.1093","volume":"32","author":[{"given":"Pradeep Anand","family":"Ravindranath","sequence":"first","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"}]},{"given":"Michel F.","family":"Sanner","sequence":"additional","affiliation":[{"name":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,6,26]]},"reference":[{"key":"2023020113451315100_btw367-B1","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1002\/jcc.23905","article-title":"DOCK 6: Impact of new features and current docking performance","volume":"36","author":"Allen","year":"2015","journal-title":"J Comput Chem"},{"key":"2023020113451315100_btw367-B2","first-page":"31","article-title":"Comprehensive identification of \u201cdruggable\u201d protein ligand binding sites","volume":"15","author":"An","year":"2004","journal-title":"Genome Inform"},{"key":"2023020113451315100_btw367-B3","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1021\/ci600253e","article-title":"A common reference framework for analyzing\/comparing proteins and ligands. 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