{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T21:16:20Z","timestamp":1717708580623},"reference-count":33,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2003,5,1]],"date-time":"2003-05-01T00:00:00Z","timestamp":1051747200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2003,5]]},"DOI":"10.1016\/s1476-9271(03)00022-7","type":"journal-article","created":{"date-parts":[[2003,6,20]],"date-time":"2003-06-20T22:47:16Z","timestamp":1056149236000},"page":"93-102","source":"Crossref","is-referenced-by-count":13,"title":["Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution"],"prefix":"10.1016","volume":"27","author":[{"given":"Kuang","family":"Lin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens","family":"Kleinjung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William R","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaap","family":"Heringa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/S1476-9271(03)00022-7_BIB1","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1006\/jmbi.1997.1287","article-title":"Do aligned sequences share the same fold?","volume":"273","author":"Abagyan","year":"1997","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB2","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/0022-2836(91)90193-A","article-title":"Amino acid substitution matrices from an information theoretic perspective","volume":"219","author":"Altschul","year":"1991","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB3","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1093\/bioinformatics\/15.11.937","article-title":"Exploiting the past and the future in protein secondary structure prediction","volume":"15","author":"Baldi","year":"1999","journal-title":"Bioinformatics"},{"key":"10.1016\/S1476-9271(03)00022-7_BIB4","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1093\/protein\/7.11.1323","article-title":"Amino acid substitution during functionally constrained divergent evolution of protein sequences","volume":"7","author":"Benner","year":"1994","journal-title":"Protein Eng."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB5","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0022-2836(77)80200-3","article-title":"The protein data bank: a computer-based archival file for macromolecular structures","volume":"112","author":"Bernstein","year":"1977","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB6","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1002\/j.1460-2075.1986.tb04288.x","article-title":"The relation between the divergence of sequence and structure in proteins","volume":"5","author":"Chothia","year":"1986","journal-title":"EMBO J."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB7","first-page":"345","article-title":"A model of evolutionary change in proteins","volume":"5","author":"Dayhoff","year":"1978"},{"key":"10.1016\/S1476-9271(03)00022-7_BIB8","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1002\/prot.1173","article-title":"Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations","volume":"Suppl. 5","author":"Fariselli","year":"2001","journal-title":"Proteins: Struct. Func. Gen."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB9","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1093\/protein\/9.2.133","article-title":"Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence","volume":"9","author":"Frishman","year":"1996","journal-title":"Protein Eng."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB10","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1016\/S0022-2836(02)00992-0","article-title":"Quantifying the similarities within fold space","volume":"323","author":"Harrison","year":"2002","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB11","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1002\/prot.340170108","article-title":"Performance evaluation of amino acid substitution matrices","volume":"17","author":"Henikoff","year":"1993","journal-title":"Proteins: Struct. Func. Gen."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB12","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/S0097-8485(99)00012-1","article-title":"Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment","volume":"23","author":"Heringa","year":"1999","journal-title":"Comp. Chem."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB13","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/S0097-8485(02)00008-6","article-title":"Local weighting schemes of protein multiple sequence alignment","volume":"26","author":"Heringa","year":"2002","journal-title":"Comp. Chem."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB14","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/0022-2836(91)90388-M","article-title":"Side-chain clusters in protein structures and their role in protein folding","volume":"220","author":"Heringa","year":"1991","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB15","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1093\/protein\/8.1.21","article-title":"Increasing thermal stability of subtilisin from mutations suggested by strongly interacting side-chain clusters","volume":"8","author":"Heringa","year":"1995","journal-title":"Protein Eng."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB16","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1002\/(SICI)1097-0134(1999)37:3+<15::AID-PROT4>3.0.CO;2-Z","article-title":"RMS coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions","volume":"Suppl. 3","author":"Hubbard","year":"1999","journal-title":"Proteins: Struct. Func. Gen."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB17","first-page":"275","article-title":"The rapid generation of mutation data matrices from protein sequences","volume":"8","author":"Jones","year":"1992","journal-title":"Comput. Appl. Biosci."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB18","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"10.1016\/S1476-9271(03)00022-7_BIB19","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1016\/S0022-2836(02)00971-3","article-title":"Sequence variations within protein families are linearly related to structural variations","volume":"323","author":"Koehl","year":"2002","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB20","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. Graphics"},{"key":"10.1016\/S1476-9271(03)00022-7_BIB21","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1107\/S0021889891004399","article-title":"molscript: a program to produce both detailed and schematic plots of protein structures","volume":"24","author":"Kraulis","year":"1991","journal-title":"J. Appl. Crystallogr."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB22","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1093\/bioinformatics\/18.10.1350","article-title":"Threading Using Neural nEtwork (TUNE): the measure of protein sequence-structure compatibility","volume":"18","author":"Lin","year":"2002","journal-title":"Bioinformatics"},{"key":"10.1016\/S1476-9271(03)00022-7_BIB23","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1002\/pro.5560071126","article-title":"homstrad: a database of protein structure alignments for homologous families","volume":"7","author":"Mizuguchi","year":"1998","journal-title":"Protein Sci."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB24","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1089\/10665270050514918","article-title":"Modeling amino acid replacement","volume":"7","author":"Muller","year":"2000","journal-title":"J. Comput. Biol."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB25","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1002\/prot.340140203","article-title":"Fast structure alignment for protein databank searching","volume":"14","author":"Orengo","year":"1992","journal-title":"Proteins: Struct. Func. Gen."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB26","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1016\/S0969-2126(97)00260-8","article-title":"cath\u2014a hierarchic classification of protein domain structures","volume":"5","author":"Orengo","year":"1997","journal-title":"Structure"},{"key":"10.1016\/S1476-9271(03)00022-7_BIB27","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1002\/prot.340090107","article-title":"Database of homology derived protein structures and the structural meaning of sequence alignment","volume":"9","author":"Sander","year":"1991","journal-title":"Proteins: Struct. Func. Gen."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB28","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1093\/protein\/15.9.721","article-title":"Prediction of protein residue contacts with a PDB-derived likelihood matrix","volume":"15","author":"Singer","year":"2002","journal-title":"Protein Eng."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB29","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1110\/ps.8.3.654","article-title":"Protein structure comparison using iterated double dynamic programming","volume":"8","author":"Taylor","year":"1999","journal-title":"Protein Sci."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB30","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":"10.1016\/S1476-9271(03)00022-7_BIB31","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1093\/bioinformatics\/15.1.87","article-title":"BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs","volume":"15","author":"Thompson","year":"1999","journal-title":"Bioinformatics"},{"key":"10.1016\/S1476-9271(03)00022-7_BIB32","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/S1476-9271(03)00022-7_BIB33","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1002\/prot.10052","article-title":"Processing and evaluation of predictions in CASP4","volume":"Suppl. 5","author":"Zemla","year":"2001","journal-title":"Proteins: Struct. Func. Gen."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927103000227?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927103000227?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2020,3,22]],"date-time":"2020-03-22T08:39:14Z","timestamp":1584866354000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927103000227"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,5]]},"references-count":33,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2003,5]]}},"alternative-id":["S1476927103000227"],"URL":"https:\/\/doi.org\/10.1016\/s1476-9271(03)00022-7","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2003,5]]}}}