{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T07:10:55Z","timestamp":1707894655948},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3431,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Identification of correlated amino acids in proteins has been a topic of broad interest in view of its functional implications and importance in protein design. A new set of pair-to-pair (P2P) substitution matrices for amino acids was recently introduced as a useful tool for inferring information on such correlated sites. We present a website developed for automated application of these matrices for analysis of query sequences. The site offers options for graphical analysis of correlations, as well as visualization of correlated amino acids on representative, structurally characterized, members of the examined family of sequences.<\/jats:p><jats:p>Availability: \u00a0http:\/\/www.ccbb.pitt.edu\/p2p<\/jats:p><jats:p>Contact: \u00a0eyal@ccbb.pitt.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm256","type":"journal-article","created":{"date-parts":[[2007,5,13]],"date-time":"2007-05-13T00:28:37Z","timestamp":1179016117000},"page":"1837-1839","source":"Crossref","is-referenced-by-count":4,"title":["Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices"],"prefix":"10.1093","volume":"23","author":[{"given":"Eran","family":"Eyal","sequence":"first","affiliation":[{"name":"1 Department of Computational Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA and 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shmuel","family":"Pietrokovski","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA and 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivet","family":"Bahar","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA and 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,5,12]]},"reference":[{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"W64","DOI":"10.1093\/nar\/gkh451","article-title":"CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences","volume":"32","author":"Afonnikov","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/0022-2836(87)90352-4","article-title":"Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus","volume":"193","author":"Altschuh","year":"1987","journal-title":"J. Mol. Biol."},{"key":"2023041105224858600_","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":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1002\/prot.21223","article-title":"A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction","volume":"67","author":"Eyal","year":"2007","journal-title":"Proteins"},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.jmb.2004.04.064","article-title":"An evolutionary conserved network of amino acids mediates gating in voltage dependent potassium channels","volume":"340","author":"Fleishman","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1002\/prot.20098","article-title":"Influence of conservation on calculations of amino acid covariance in multiple sequence alignments","volume":"56","author":"Fodor","year":"2004","journal-title":"Proteins"},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1002\/prot.340180402","article-title":"Correlated mutations and residue contacts in proteins","volume":"18","author":"Gobel","year":"1994","journal-title":"Proteins"},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1002\/prot.20933","article-title":"Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families","volume":"63","author":"Halperin","year":"2006","journal-title":"Proteins"},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1016\/0022-2836(94)90032-9","article-title":"Position-based sequence weights","volume":"243","author":"Henikoff","year":"1994","journal-title":"J. Mol. Biol."},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1093\/bioinformatics\/15.6.471","article-title":"Blocks+: a non-redundant database of protein alignment blocks dervied from multiple compilations","volume":"15","author":"Henikoff","year":"1999","journal-title":"Bioinformatics"},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1002\/prot.10180","article-title":"Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations","volume":"48","author":"Kass","year":"2002","journal-title":"Proteins"},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1186\/1471-2105-7-503","article-title":"Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives","volume":"7","author":"Kundrotas","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023041105224858600_","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1073\/pnas.91.1.98","article-title":"How frequent are correlated changes in families of protein sequences?","volume":"91","author":"Neher","year":"1994","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023041105224858600_","first-page":"319","article-title":"A graphical interface for correlated mutations and other protein structure prediction methods","volume":"13","author":"Pazos","year":"1997","journal-title":"Comput. Appl. Biosci."},{"key":"2023041105224858600_","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 alignment through sequence weighting, position-specific gap penalties and weight matrix choice","volume":"22","author":"Thompson","year":"1994","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/14\/1837\/49813120\/bioinformatics_23_14_1837.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/14\/1837\/49813120\/bioinformatics_23_14_1837.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T06:53:40Z","timestamp":1707893620000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/14\/1837\/190358"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,5,12]]},"references-count":15,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2007,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm256","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,7,15]]},"published":{"date-parts":[[2007,5,12]]}}}