{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,9]],"date-time":"2024-05-09T07:53:55Z","timestamp":1715241235400},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1635,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The differences between observed and predicted 13C\u03b1 chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. For this reason, we previously introduced CheShift, a Web server for protein structure validation. Now, we present CheShift-2 in which a graphical user interface is implemented to render such local flaws easily visible. A series of applications to 15 ensembles of conformations illustrate the ability of CheShift-2 to locate the main structural flaws rapidly and accurately on a per-residue basis. Since accuracy plays a central role in CheShift predictions, the treatment of histidine (His) is investigated here by exploring which form of His should be used in CheShift-2.<\/jats:p>\n               <jats:p>Availability: \u00a0CheShift-2 is free of charge for academic use and can be accessed from www.cheshift.com<\/jats:p>\n               <jats:p>Contact: \u00a0has5@cornell.edu; jv84@cornell.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at the Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts179","type":"journal-article","created":{"date-parts":[[2012,4,12]],"date-time":"2012-04-12T05:16:27Z","timestamp":1334207787000},"page":"1538-1539","source":"Crossref","is-referenced-by-count":23,"title":["<i>Che<\/i>Shift-2: graphic validation of protein structures"],"prefix":"10.1093","volume":"28","author":[{"given":"Osvaldo A.","family":"Martin","sequence":"first","affiliation":[{"name":"1 Universidad Nacional de San Luis, IMASL-CONICET, Ej\u00e9rcito de Los Andes, 950-5700 San Luis, Argentina and 2Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA"}]},{"given":"Jorge A.","family":"Vila","sequence":"additional","affiliation":[{"name":"1 Universidad Nacional de San Luis, IMASL-CONICET, Ej\u00e9rcito de Los Andes, 950-5700 San Luis, Argentina and 2Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA"},{"name":"1 Universidad Nacional de San Luis, IMASL-CONICET, Ej\u00e9rcito de Los Andes, 950-5700 San Luis, Argentina and 2Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA"}]},{"given":"Harold A.","family":"Scheraga","sequence":"additional","affiliation":[{"name":"1 Universidad Nacional de San Luis, IMASL-CONICET, Ej\u00e9rcito de Los Andes, 950-5700 San Luis, Argentina and 2Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,4,11]]},"reference":[{"key":"2023012512313254600_B1","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":"2023012512313254600_B2","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1002\/prot.21165","article-title":"Evaluating protein structures determined by structural genomics consortia","volume":"66","author":"Bhattacharya","year":"2007","journal-title":"Proteins"},{"key":"2023012512313254600_B3","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1021\/ja047109h","article-title":"Protein NMR Recall, Precision and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics","volume":"127","author":"Huang","year":"2005","journal-title":"J. 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