{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:43:31Z","timestamp":1772171011091,"version":"3.50.1"},"reference-count":34,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2008,10,3]],"date-time":"2008-10-03T00:00:00Z","timestamp":1222992000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000179","type":"journal-article","created":{"date-parts":[[2008,10,2]],"date-time":"2008-10-02T18:21:30Z","timestamp":1222971690000},"page":"e1000179","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures"],"prefix":"10.1371","volume":"4","author":[{"given":"Sungsam","family":"Gong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom L.","family":"Blundell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2008,10,3]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1038\/217624a0","article-title":"Evolutionary rate at the molecular level.","volume":"217","author":"M Kimura","year":"1968","journal-title":"Nature"},{"key":"ref2","article-title":"Atlas of Protein Sequence and Structure. Volume 3","author":"MO Dayhoff","year":"1968"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"10915","DOI":"10.1073\/pnas.89.22.10915","article-title":"Amino acid substitution matrices from protein blocks.","volume":"89","author":"S Henikoff","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref4","first-page":"275","article-title":"The rapid generation of mutation data matrices from protein sequences.","volume":"8","author":"DT Jones","year":"1992","journal-title":"Comput Appl Biosci"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1093\/oxfordjournals.molbev.a003851","article-title":"A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.","volume":"18","author":"S Whelan","year":"2001","journal-title":"Mol Biol Evol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/0022-5193(65)90083-4","article-title":"Molecules as documents of evolutionary history.","volume":"8","author":"E Zuckerkandl","year":"1965","journal-title":"J Theor Biol"},{"key":"ref7","first-page":"189","article-title":"Molecular disease, evolution, and genetic heterogeneity.","author":"E Zuckerkandl","year":"1962"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1016\/j.jmb.2004.08.022","article-title":"Distinguishing structural and functional restraints in evolution in order to identify interaction sites.","volume":"342","author":"V Chelliah","year":"2004","journal-title":"J Mol Biol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1002\/pro.5560010203","article-title":"Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.","volume":"1","author":"J Overington","year":"1992","journal-title":"Protein Sci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1098\/rspb.1990.0077","article-title":"Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction.","volume":"241","author":"J Overington","year":"1990","journal-title":"Proc Biol Sci"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1006\/jmbi.2001.4762","article-title":"FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.","volume":"310","author":"J Shi","year":"2001","journal-title":"J Mol Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1002\/prot.20617","article-title":"Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition.","volume":"61","author":"V Chelliah","year":"2005","journal-title":"Proteins"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1006\/jmbi.1994.1330","article-title":"Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures.","volume":"238","author":"H Wako","year":"1994","journal-title":"J Mol Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1006\/jmbi.1993.1323","article-title":"Alignment and searching for common protein folds using a data bank of structural templates.","volume":"231","author":"MS Johnson","year":"1993","journal-title":"J Mol Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1006\/jmbi.1997.0924","article-title":"A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence.","volume":"267","author":"DW Rice","year":"1997","journal-title":"J Mol Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"D129","DOI":"10.1093\/nar\/gkh028","article-title":"The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.","volume":"32","author":"CT Porter","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"D115","DOI":"10.1093\/nar\/gkh131","article-title":"UniProt: the Universal Protein knowledgebase.","volume":"32","author":"R Apweiler","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/1471-2105-6-207","article-title":"A protein domain interaction interface database: InterPare.","volume":"6","author":"S Gong","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures.","volume":"247","author":"AG Murzin","year":"1995","journal-title":"J Mol Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1006\/jmbi.1994.1334","article-title":"Satisfying hydrogen bonding potential in proteins.","volume":"238","author":"IK McDonald","year":"1994","journal-title":"J Mol Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/jmbi.1998.1843","article-title":"Anatomy of hot spots in protein interfaces.","volume":"280","author":"AA Bogan","year":"1998","journal-title":"J Mol Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"15447","DOI":"10.1073\/pnas.0505425102","article-title":"Conservation and relative importance of residues across protein-protein interfaces.","volume":"102","author":"M Guharoy","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"4917","DOI":"10.1074\/jbc.274.8.4917","article-title":"Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography.","volume":"274","author":"BA Fox","year":"1999","journal-title":"J Biol Chem"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"21913","DOI":"10.1074\/jbc.M109398200","article-title":"Structural and functional analysis of the human mitotic-specific ubiquitin-conjugating enzyme, UbcH10.","volume":"277","author":"Y Lin","year":"2002","journal-title":"J Biol Chem"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1006\/jmbi.1996.0167","article-title":"An evolutionary trace method defines binding surfaces common to protein families.","volume":"257","author":"O Lichtarge","year":"1996","journal-title":"J Mol Biol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/0968-0004(90)90036-B","article-title":"From comparisons of protein sequences and structures to protein modelling and design.","volume":"15","author":"A Sali","year":"1990","journal-title":"Trends Biochem Sci"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank.","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.","volume":"22","author":"W Li","year":"2006","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1471-2105-6-31","article-title":"Automated generation of heuristics for biological sequence comparison.","volume":"6","author":"GS Slater","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref30","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":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1093\/bioinformatics\/14.7.617","article-title":"JOY: protein sequence-structure representation and analysis.","volume":"14","author":"K Mizuguchi","year":"1998","journal-title":"Bioinformatics"},{"key":"ref32","article-title":"All-atom small-probe contact surface analysis: An information-rich description of molecular goodness-of-fit [PhD thesis]","author":"MJ Word","year":"2000"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1016\/S0092-8674(01)00618-3","article-title":"Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.","volume":"107","author":"C Hoang","year":"2001","journal-title":"Cell"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1006\/jmbi.2000.3799","article-title":"A revised mechanism for the alkaline phosphatase reaction involving three metal ions.","volume":"299","author":"B Stec","year":"2000","journal-title":"J Mol Biol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000179","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T16:51:15Z","timestamp":1540313475000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000179"}},"subtitle":[],"editor":[{"given":"Michael","family":"Levitt","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2008,10,3]]},"references-count":34,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2008,10,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000179","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.1129803.586883","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,3]]}}}