{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:31:49Z","timestamp":1767961909385,"version":"3.49.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"suppl_2","license":[{"start":{"date-parts":[[2016,11,14]],"date-time":"2016-11-14T00:00:00Z","timestamp":1479081600000},"content-version":"vor","delay-in-days":2011,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"DOI":"10.1093\/nar\/gkr356","type":"journal-article","created":{"date-parts":[[2011,5,17]],"date-time":"2011-05-17T04:20:10Z","timestamp":1305606010000},"page":"W242-W248","source":"Crossref","is-referenced-by-count":94,"title":["DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins"],"prefix":"10.1093","volume":"39","author":[{"given":"Kuan Pern","family":"Tan","sequence":"first","affiliation":[]},{"given":"Raghavan","family":"Varadarajan","sequence":"additional","affiliation":[]},{"given":"M. S.","family":"Madhusudhan","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2011,5,14]]},"reference":[{"key":"key\n\t\t\t\t20170720162947_B1","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/S0969-2126(99)80097-5","article-title":"Residue depth: a novel parameter for the analysis of protein structure and stability","volume":"7","author":"Chakravarty","year":"1999","journal-title":"Structure"},{"key":"key\n\t\t\t\t20170720162947_B2","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/0022-2836(71)90324-X","article-title":"The interpretation of protein structures: estimation of static accessibility","volume":"55","author":"Lee","year":"1971","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720162947_B3","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1016\/0022-2836(91)90722-I","article-title":"A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution","volume":"218","author":"Pedersen","year":"1991","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720162947_B4","doi-asserted-by":"crossref","first-page":"2553","DOI":"10.1016\/S0006-3495(03)75060-7","article-title":"Atom depth as a descriptor of the protein interior","volume":"84","author":"Pintar","year":"2003","journal-title":"Biophys. J."},{"key":"key\n\t\t\t\t20170720162947_B5","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/j.tibs.2003.09.004","article-title":"Atom depth in protein structure and function","volume":"28","author":"Pintar","year":"2003","journal-title":"Trends Biochem. Sci."},{"key":"key\n\t\t\t\t20170720162947_B6","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1002\/prot.20529","article-title":"The \u2018first in-last out\u2019 hypothesis on protein folding revisited","volume":"60","author":"Pintar","year":"2005","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170720162947_B7","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1074\/mcp.M400159-MCP200","article-title":"Pocketome via comprehensive identification and classification of ligand binding envelopes","volume":"4","author":"An","year":"2005","journal-title":"Mol. Cell. Proteomics"},{"key":"key\n\t\t\t\t20170720162947_B8","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1023\/A:1008124202956","article-title":"Fast prediction and visualization of protein binding pockets with PASS","volume":"14","author":"Brady","year":"2000","journal-title":"J. Comput. Aided Mol. Des."},{"key":"key\n\t\t\t\t20170720162947_B9","doi-asserted-by":"crossref","first-page":"e1000585","DOI":"10.1371\/journal.pcbi.1000585","article-title":"Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure","volume":"5","author":"Capra","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20170720162947_B10","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/0263-7855(93)85003-9","article-title":"A new approach to the automatic identification of candidates for ligand receptor sites in proteins: (I). Search for pocket regions","volume":"11","author":"Del Carpio","year":"1993","journal-title":"J. Mol. Graph."},{"key":"key\n\t\t\t\t20170720162947_B11","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/0263-7855(92)80052-F","article-title":"Finding and filling protein cavities using cellular logic operations","volume":"10","author":"Delaney","year":"1992","journal-title":"J. Mol. Graph."},{"key":"key\n\t\t\t\t20170720162947_B12","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/S1093-3263(98)00002-3","article-title":"LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins","volume":"15","author":"Hendlich","year":"1997","journal-title":"J. Mol. Graph. Model."},{"key":"key\n\t\t\t\t20170720162947_B13","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1007\/BF00117400","article-title":"Cavity search: an algorithm for the isolation and display of cavity-like binding regions","volume":"4","author":"Ho","year":"1990","journal-title":"J. Comput. Aided Mol. Des."},{"key":"key\n\t\t\t\t20170720162947_B14","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1107\/S0907444993011333","article-title":"Detection, delineation, measurement and display of cavities in macromolecular structures","volume":"50","author":"Kleywegt","year":"1994","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"key\n\t\t\t\t20170720162947_B15","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/0263-7855(95)00073-9","article-title":"SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions","volume":"13","author":"Laskowski","year":"1995","journal-title":"J. Mol. Graph."},{"key":"key\n\t\t\t\t20170720162947_B16","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1093\/bioinformatics\/bti315","article-title":"Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites","volume":"21","author":"Laurie","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720162947_B17","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/1471-2105-10-168","article-title":"Fpocket: an open source platform for ligand pocket detection","volume":"10","author":"Le Guilloux","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720162947_B18","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/0263-7855(92)80074-N","article-title":"POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids","volume":"10","author":"Levitt","year":"1992","journal-title":"J. Mol. Graph."},{"key":"key\n\t\t\t\t20170720162947_B19","doi-asserted-by":"crossref","first-page":"1884","DOI":"10.1002\/pro.5560070905","article-title":"Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design","volume":"7","author":"Liang","year":"1998","journal-title":"Protein Sci."},{"key":"key\n\t\t\t\t20170720162947_B20","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1016\/0263-7855(95)00071-2","article-title":"Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations","volume":"13","author":"Masuya","year":"1995","journal-title":"J. Mol. Graph."},{"key":"key\n\t\t\t\t20170720162947_B21","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1006\/jmbi.1996.0077","article-title":"The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria","volume":"256","author":"Peters","year":"1996","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720162947_B22","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/S1093-3263(02)00164-X","article-title":"LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites","volume":"21","author":"Venkatachalam","year":"2003","journal-title":"J. Mol. Graph. Model."},{"key":"key\n\t\t\t\t20170720162947_B23","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1752-153X-1-7","article-title":"PocketPicker: analysis of ligand binding-sites with shape descriptors","volume":"1","author":"Weisel","year":"2007","journal-title":"Chem. Cent. J."},{"key":"key\n\t\t\t\t20170720162947_B24","doi-asserted-by":"crossref","first-page":"1550","DOI":"10.2174\/092986710790979944","article-title":"In silico prediction of binding sites on proteins","volume":"17","author":"Leis","year":"2010","journal-title":"Curr. Med. Chem."},{"key":"key\n\t\t\t\t20170720162947_B25","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1021\/ci1000289","article-title":"Large-scale comparison of four binding site detection algorithms","volume":"50","author":"Schmidtke","year":"2010","journal-title":"J. Chem. Inf. Model"},{"key":"key\n\t\t\t\t20170720162947_B26","doi-asserted-by":"crossref","first-page":"6269","DOI":"10.1021\/j100308a038","article-title":"The missing term in effective pair potentials","volume":"91","author":"Berendsen","year":"1987","journal-title":"J. Phys. Chem."},{"key":"key\n\t\t\t\t20170720162947_B27","volume-title":"In Intermolecular Forces","author":"Berendsen","year":"1981"},{"key":"key\n\t\t\t\t20170720162947_B28","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/0022-2836(73)90011-9","article-title":"Environment and exposure to solvent of protein atoms. Lysozyme and insulin","volume":"79","author":"Shrake","year":"1973","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720162947_B29","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1093\/protein\/1.3.159","article-title":"Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling","volume":"1","author":"Hubbard","year":"1987","journal-title":"Protein Eng."},{"key":"key\n\t\t\t\t20170720162947_B30","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720162947_B31","doi-asserted-by":"crossref","first-page":"D667","DOI":"10.1093\/nar\/gkm839","article-title":"LigASite\u2013a database of biologically relevant binding sites in proteins with known apo-structures","volume":"36","author":"Dessailly","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720162947_B32","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/S0968-0004(98)01253-5","article-title":"PQS: a protein quaternary structure file server","volume":"23","author":"Henrick","year":"1998","journal-title":"Trends Biochem. Sci."},{"key":"key\n\t\t\t\t20170720162947_B33","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/0005-2795(75)90109-9","article-title":"Comparison of the predicted and observed secondary structure of T4 phage lysozyme","volume":"405","author":"Matthews","year":"1975","journal-title":"Biochim. Biophys. Acta"},{"key":"key\n\t\t\t\t20170720162947_B34","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/nsmb1073","article-title":"Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus","volume":"13","author":"Erbel","year":"2006","journal-title":"Nat. Struct. Mol. Biol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/39\/suppl_2\/W242\/18783554\/gkr356.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:42:19Z","timestamp":1522680139000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkr356"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,14]]},"references-count":34,"journal-issue":{"issue":"suppl_2","published-online":{"date-parts":[[2011,5,14]]},"published-print":{"date-parts":[[2011,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkr356","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,5,14]]}}}