{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,25]],"date-time":"2025-12-25T19:24:16Z","timestamp":1766690656880},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The ability to reliably predict protein\u2013protein and protein\u2013ligand interactions is important for identifying druggable binding sites and for understanding how proteins communicate. Most currently available algorithms identify cavities on the protein surface as potential ligand recognition sites. The method described here does not explicitly look for cavities but uses small surface patches consisting of triplets of adjacent surface atomic groups that can be touched simultaneously by a probe sphere representing a solvent molecule. A total of 455 different types of triplets can be identified. A training set of 309 protein\u2013ligand protein X-ray structures has been used to generate interface propensities for the triplets, which can be used to predict their involvement in ligand\u2013binding interactions.<\/jats:p>\n               <jats:p>Results: The success rate for locating protein\u2013ligand binding sites on protein surfaces using this new surface triplet propensities (STP) algorithm is 88% which compares well with currently available grid-based and energy-based approaches. Q-SiteFinder's dataset (Laurie and Jackson, 2005. Bioinformatics, 21, 1908\u20131916) was used to show the favorable performance of STP. An analysis of the different triplet types showed that higher ligand binding propensity is related to more polarizable surfaces. The interaction statistics between triplet atoms on the protein surface and ligand atoms have been used to estimate statistical free energies of interaction. The \u0394Gstat for halogen atoms interacting with hydrophobic triplets is \u22120.6 kcal\/mol and an estimate of the maximal \u0394Gstat for a ligand atom interacting with a triplet in a binding pocket is \u22121.45 kcal\/mol.<\/jats:p>\n               <jats:p>Availability: Freely available online at http:\/\/opus.bch.ed.ac.uk\/stp. Website implemented in Php, with all major browsers supported.<\/jats:p>\n               <jats:p>Contact: \u00a0m.walkinshaw@ed.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq490","type":"journal-article","created":{"date-parts":[[2010,9,7]],"date-time":"2010-09-07T01:44:16Z","timestamp":1283823856000},"page":"2549-2555","source":"Crossref","is-referenced-by-count":22,"title":["Identification of protein binding surfaces using surface triplet propensities"],"prefix":"10.1093","volume":"26","author":[{"given":"Wissam","family":"Mehio","sequence":"first","affiliation":[{"name":"1 Institute of Structural and Molecular Biology, School of Biological Sciences, The University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK and 2Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden"}]},{"given":"Graham J.L.","family":"Kemp","sequence":"additional","affiliation":[{"name":"1 Institute of Structural and Molecular Biology, School of Biological Sciences, The University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK and 2Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden"}]},{"given":"Paul","family":"Taylor","sequence":"additional","affiliation":[{"name":"1 Institute of Structural and Molecular Biology, School of Biological Sciences, The University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK and 2Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden"}]},{"given":"Malcolm D.","family":"Walkinshaw","sequence":"additional","affiliation":[{"name":"1 Institute of Structural and Molecular Biology, School of Biological Sciences, The University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK and 2Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2010,9,6]]},"reference":[{"key":"2023012507541727000_B1","doi-asserted-by":"crossref","first-page":"7927","DOI":"10.1021\/jm901566c","article-title":"Evaluation of di-sansalvamide a derivatives: synthesis, structure-activity relationship, and mechanism of action","volume":"52","author":"Alexander","year":"2009","journal-title":"J. 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