{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T03:45:04Z","timestamp":1773805504437,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,5]],"date-time":"2016-10-05T00:00:00Z","timestamp":1475625600000},"content-version":"vor","delay-in-days":1588,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,1]]},"DOI":"10.1093\/nar\/gks481","type":"journal-article","created":{"date-parts":[[2012,6,2]],"date-time":"2012-06-02T00:24:03Z","timestamp":1338596643000},"page":"W249-W256","source":"Crossref","is-referenced-by-count":48,"title":["DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry"],"prefix":"10.1093","volume":"40","author":[{"given":"Yao Chi","family":"Chen","sequence":"first","affiliation":[]},{"given":"Jon D.","family":"Wright","sequence":"additional","affiliation":[]},{"given":"Carmay","family":"Lim","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,5,31]]},"reference":[{"key":"key\n\t\t\t\t20170720163421_gks481-B1","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.mcn.2007.03.007","article-title":"TDP43 is a human low molecular weight neurofilament (hNFL) mRNA-binding protein","volume":"35","author":"Strong","year":"2007","journal-title":"Mol. Cell. Neurosci."},{"key":"key\n\t\t\t\t20170720163421_gks481-B2","doi-asserted-by":"crossref","first-page":"2556","DOI":"10.1101\/gad.7.12b.2556","article-title":"The DNA-binding domain of p53 contains the four conserved regions and the major mutation hot spots","volume":"7","author":"Pavletich","year":"1993","journal-title":"Genes Dev."},{"key":"key\n\t\t\t\t20170720163421_gks481-B3","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1093\/bioinformatics\/btg432","article-title":"Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information","volume":"20","author":"Ahmad","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B4","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1002\/jcc.10361","article-title":"Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network","volume":"25","author":"Keil","year":"2004","journal-title":"J. Comput. Chem."},{"key":"key\n\t\t\t\t20170720163421_gks481-B5","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1471-2105-6-33","article-title":"PSSM-based prediction of DNA binding sites in proteins","volume":"6","author":"Ahmad","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B6","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1186\/1471-2105-7-262","article-title":"Predicting DNA-binding sites of proteins from amino acid sequence","volume":"7","author":"Yan","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B7","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1002\/prot.20977","article-title":"Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins","volume":"64","author":"Kuznetsov","year":"2006","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170720163421_gks481-B8","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1093\/bioinformatics\/btl672","article-title":"DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins","volume":"23","author":"Hwang","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B9","doi-asserted-by":"crossref","first-page":"i347","DOI":"10.1093\/bioinformatics\/btm174","article-title":"Prediction of DNA-binding residues from sequence","volume":"23","author":"Ofran","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B10","doi-asserted-by":"crossref","first-page":"W396","DOI":"10.1093\/nar\/gkp449","article-title":"ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors","volume":"37","author":"Chu","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B11","doi-asserted-by":"crossref","first-page":"W243","DOI":"10.1093\/nar\/gkl298","article-title":"BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences","volume":"34","author":"Wang","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B12","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/1752-0509-4-S1-S3","article-title":"BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features","volume":"4","author":"Wang","year":"2010","journal-title":"BMC Syst. Biol."},{"key":"key\n\t\t\t\t20170720163421_gks481-B13","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1093\/bioinformatics\/btn583","article-title":"Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature","volume":"25","author":"Wu","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B14","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2164-10-S1-S1","article-title":"Prediction of DNA-binding residues from protein sequence information using random forest","volume":"10","author":"Wang","year":"2009","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B15","doi-asserted-by":"crossref","first-page":"W431","DOI":"10.1093\/nar\/gkq361","article-title":"NAPS: a residue-level nucleic acid-binding prediction server","volume":"38","author":"Carson","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B16","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1752-0509-5-S1-S7","article-title":"MetaDBSite: a meta approach to improve protein DNA-binding sites prediction","volume":"5","author":"Si","year":"2011","journal-title":"BMC Syst. Biol."},{"key":"key\n\t\t\t\t20170720163421_gks481-B17","doi-asserted-by":"crossref","first-page":"7189","DOI":"10.1093\/nar\/gkg922","article-title":"Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins","volume":"31","author":"Jones","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B18","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1016\/S0022-2836(03)00031-7","article-title":"Annotating nucleic acid-binding function based on protein structure","volume":"326","author":"Stawiski","year":"2003","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720163421_gks481-B19","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1002\/prot.20111","article-title":"Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces","volume":"55","author":"Tsuchiya","year":"2004","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170720163421_gks481-B20","doi-asserted-by":"crossref","first-page":"4732","DOI":"10.1093\/nar\/gkh803","article-title":"Identifying DNA-binding proteins using structural motifs and the electrostatic potential","volume":"32","author":"Shanahan","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B21","doi-asserted-by":"crossref","first-page":"3679","DOI":"10.1093\/bioinformatics\/bti575","article-title":"HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif","volume":"21","author":"Ferrer-Costa","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B22","doi-asserted-by":"crossref","first-page":"e150","DOI":"10.1093\/nar\/gkq478","article-title":"A structural-alphabet-based strategy for finding structural motifs across protein families","volume":"38","author":"Wu","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B23","doi-asserted-by":"crossref","first-page":"W417","DOI":"10.1093\/nar\/gkq396","article-title":"DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues","volume":"38","author":"Ozbek","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B24","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1093\/bioinformatics\/bti232","article-title":"PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces","volume":"21","author":"Tsuchiya","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B25","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1093\/nar\/gkm008","article-title":"DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces","volume":"35","author":"Tjong","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B26","doi-asserted-by":"crossref","first-page":"3978","DOI":"10.1093\/nar\/gkn332","article-title":"DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions","volume":"36","author":"Gao","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B27","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/prot.21366","article-title":"Predicting DNA-binding sites on proteins from electrostatic stabilization upon mutation to Asp\/Glu and evolutionary conservation","volume":"67","author":"Chen","year":"2007","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20170720163421_gks481-B28","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1093\/nar\/gkn386","article-title":"A protein\u2013DNA docking benchmark","volume":"36","author":"van Dijk","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B29","doi-asserted-by":"crossref","first-page":"7078","DOI":"10.1093\/nar\/gkn868","article-title":"Common physical basis of macromolecule-binding sites in proteins","volume":"36","author":"Chen","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B30","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1107\/S0907444902003451","article-title":"The Protein Data Bank","volume":"58","author":"Berman","year":"2002","journal-title":"Acta Crystallogr. D"},{"key":"key\n\t\t\t\t20170720163421_gks481-B31","doi-asserted-by":"crossref","first-page":"D247","DOI":"10.1093\/nar\/gki024","article-title":"The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis","volume":"33","author":"Pearl","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B32","doi-asserted-by":"crossref","first-page":"D323","DOI":"10.1093\/nar\/gkn822","article-title":"The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures","volume":"37","author":"Goldenberg","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0022-2836(89)90084-3","article-title":"Protein structure alignment","volume":"208","author":"Taylor","year":"1989","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720163421_gks481-B34","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B35","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1006\/jmbi.1994.1334","article-title":"Satisfying hydrogen bonding potential in proteins","volume":"238","author":"McDonald","year":"1994","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720163421_gks481-B36","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/0022-2836(87)90038-6","article-title":"Interior and surface of monomeric proteins","volume":"196","author":"Miller","year":"1987","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720163421_gks481-B37","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/0263-7855(96)00009-4","article-title":"MOLMOL: a program for display and analysis of macromolecular structures","volume":"14","author":"Koradi","year":"1996","journal-title":"J. Mol. Graph."},{"key":"key\n\t\t\t\t20170720163421_gks481-B38","doi-asserted-by":"crossref","first-page":"2001","DOI":"10.1110\/ps.03154503","article-title":"A graph-theory algorithm for rapid protein side-chain prediction","volume":"12","author":"Canutescu","year":"2003","journal-title":"Protein Sci."},{"key":"key\n\t\t\t\t20170720163421_gks481-B39","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs","volume":"26","author":"Case","year":"2005","journal-title":"J. Comput. Chem."},{"key":"key\n\t\t\t\t20170720163421_gks481-B40","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1002\/jcc.10349","article-title":"A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations","volume":"24","author":"Duan","year":"2003","journal-title":"J. Comput. Chem."},{"key":"key\n\t\t\t\t20170720163421_gks481-B41","doi-asserted-by":"crossref","first-page":"W529","DOI":"10.1093\/nar\/gkq399","article-title":"ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids","volume":"38","author":"Ashkenazy","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B42","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1093\/nar\/gki370","article-title":"ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures","volume":"33","author":"Landau","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163421_gks481-B43","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1093\/bioinformatics\/19.1.163","article-title":"ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information","volume":"19","author":"Glaser","year":"2003","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163421_gks481-B44","doi-asserted-by":"crossref","first-page":"e29","DOI":"10.1093\/nar\/gkn008","article-title":"Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry","volume":"36","author":"Chen","year":"2008","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/40\/W1\/W249\/18783985\/gks481.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:40:23Z","timestamp":1522680023000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gks481"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,5,31]]},"references-count":44,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2012,5,31]]},"published-print":{"date-parts":[[2012,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gks481","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,5,31]]}}}