{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T19:33:08Z","timestamp":1760297588643},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The error rate of asparagine (Asn) and glutamine (Gln) amide rotamers in protein crystal structures is in the order of 20% and as a consequence the current Protein Database (PDB) contains approximately half a million incorrect Asn and Gln side-chain rotamers. Here we present NQ-Flipper, a web service based on knowledge-based potentials of mean force to automatically detect and correct erroneous rotamers. We achieve excellent agreement with expert curated data.<\/jats:p>\n               <jats:p>Availability: The program is accessible freely as a web service at<\/jats:p>\n               <jats:p>Contact: \u00a0sippl@came.sbg.ac.at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl128","type":"journal-article","created":{"date-parts":[[2006,4,5]],"date-time":"2006-04-05T00:24:30Z","timestamp":1144196670000},"page":"1397-1398","source":"Crossref","is-referenced-by-count":27,"title":["NQ-Flipper: validation and correction of asparagine\/glutamine amide rotamers in protein crystal structures"],"prefix":"10.1093","volume":"22","author":[{"given":"Christian X.","family":"Weichenberger","sequence":"first","affiliation":[{"name":"Center of Applied Molecular Engineering, University of Salzburg \u00a0 Jakob Haringerstrasse 5, 5020 Salzburg, Austria"}]},{"given":"Manfred J.","family":"Sippl","sequence":"additional","affiliation":[{"name":"Center of Applied Molecular Engineering, University of Salzburg \u00a0 Jakob Haringerstrasse 5, 5020 Salzburg, Austria"}]}],"member":"286","published-online":{"date-parts":[[2006,4,4]]},"reference":[{"key":"2023012408404803400_b1","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1093\/bioinformatics\/16.5.412","article-title":"Assessing the accuracy of prediction algorithms for classification: an overview","volume":"16","author":"Baldi","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012408404803400_b2","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":"2023012408404803400_b3","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/381272a0","article-title":"Errors in protein structures","volume":"381","author":"Hooft","year":"1996","journal-title":"Nature"},{"key":"2023012408404803400_b4","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1002\/prot.10286","article-title":"Structure validation by Calpha geometry: phi, psi and Cbeta deviation","volume":"50","author":"Lovell","year":"2003","journal-title":"Proteins"},{"key":"2023012408404803400_b5","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1093\/protein\/8.3.217","article-title":"The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains","volume":"8","author":"McDonald","year":"1995","journal-title":"Protein Eng."},{"key":"2023012408404803400_b6","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1016\/S0022-2836(05)80269-4","article-title":"Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins","volume":"213","author":"Sippl","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2023012408404803400_b7","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1006\/jmbi.1998.2401","article-title":"Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation","volume":"285","author":"Word","year":"1999","journal-title":"J. Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/11\/1397\/48838568\/bioinformatics_22_11_1397.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/11\/1397\/48838568\/bioinformatics_22_11_1397.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T08:41:38Z","timestamp":1674549698000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/11\/1397\/239014"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,4,4]]},"references-count":7,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2006,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl128","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,6,1]]},"published":{"date-parts":[[2006,4,4]]}}}