{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T13:11:01Z","timestamp":1780405861444,"version":"3.54.1"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein assemblies are currently poorly represented in structural databases and their structural elucidation is a key goal in biology. Here we analyse clefts in protein surfaces, likely to correspond to binding \u2018hot-spots\u2019, and rank them according to sequence conservation and simple measures of physical properties including hydrophobicity, desolvation, electrostatic and van der Waals potentials, to predict which are involved in binding in the native complex.<\/jats:p>\n               <jats:p>Results: The resulting differences between predicting binding-sites at protein\u2013protein and protein\u2013ligand interfaces are striking. There is a high level of prediction accuracy (\u226493%) for protein\u2013ligand interactions, based on the following attributes: van der Waals potential, electrostatic potential, desolvation and surface conservation. Generally, the prediction accuracy for protein\u2013protein interactions is lower, with the exception of enzymes. Our results show that the ease of cleft desolvation is strongly predictive of interfaces and strongly maintained across all classes of protein-binding interface.<\/jats:p>\n               <jats:p>Contact: \u00a0r.m.jackson@leeds.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl079","type":"journal-article","created":{"date-parts":[[2006,3,8]],"date-time":"2006-03-08T02:23:26Z","timestamp":1141784606000},"page":"1335-1342","source":"Crossref","is-referenced-by-count":138,"title":["Predicting protein interaction sites: binding hot-spots in protein\u2013protein and protein\u2013ligand interfaces"],"prefix":"10.1093","volume":"22","author":[{"given":"Nicholas J.","family":"Burgoyne","sequence":"first","affiliation":[{"name":"Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds \u00a0 Leeds LS2 9JT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard M.","family":"Jackson","sequence":"additional","affiliation":[{"name":"Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds \u00a0 Leeds LS2 9JT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2006,3,7]]},"reference":[{"key":"2023012408412992100_b1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012408412992100_b2","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1021\/ja993784t","article-title":"Theoretical study of electron transfer between the photolyase catalytic cofactor FADH(\u2212) and DNA thymine dimer","volume":"122","author":"Antony","year":"2000","journal-title":"J. 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