{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T23:43:08Z","timestamp":1722814988845},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The clarification of linkage between protein structure and function is still a demanding process and can be supported by comparison of spatial residue patterns, so-called structural motifs. However, versatile up-to-date resources to search for local structure similarities are rare. We present Fit3D, an easily accessible web application for highly accurate screening of structural motifs in 3D protein data.<\/jats:p>\n               <jats:p>Availability and implementation: The web application is accessible at https:\/\/biosciences.hs-mittweida.de\/fit3d and program sources of the command line version were released under the terms of GNU GPLv3. Platform-independent binaries and documentations for offline usage are available at https:\/\/bitbucket.org\/fkaiser\/fit3d.<\/jats:p>\n               <jats:p>Contact: \u00a0florian.kaiser@hs-mittweida.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv637","type":"journal-article","created":{"date-parts":[[2015,10,31]],"date-time":"2015-10-31T02:38:11Z","timestamp":1446259091000},"page":"792-794","source":"Crossref","is-referenced-by-count":10,"title":["Fit3D: a web application for highly accurate screening of spatial residue patterns in protein structure data"],"prefix":"10.1093","volume":"32","author":[{"given":"Florian","family":"Kaiser","sequence":"first","affiliation":[{"name":"Department of Applied Computer and Biosciences, University of Applied Sciences Mittweida, 09648 Mittweida, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Eisold","sequence":"additional","affiliation":[{"name":"Department of Applied Computer and Biosciences, University of Applied Sciences Mittweida, 09648 Mittweida, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Bittrich","sequence":"additional","affiliation":[{"name":"Department of Applied Computer and Biosciences, University of Applied Sciences Mittweida, 09648 Mittweida, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dirk","family":"Labudde","sequence":"additional","affiliation":[{"name":"Department of Applied Computer and Biosciences, University of Applied Sciences Mittweida, 09648 Mittweida, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,30]]},"reference":[{"key":"2023020110450069900_btv637-B1","doi-asserted-by":"crossref","first-page":"D521","DOI":"10.1093\/nar\/gkt1130","article-title":"The structure\u2013function linkage database","volume":"42","author":"Akiva","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020110450069900_btv637-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":"2023020110450069900_btv637-B3","article-title":"PV\u2014WebGL-based protein viewer","author":"Biasini","year":"2014","journal-title":"Zenodo"},{"key":"2023020110450069900_btv637-B4","first-page":"1","article-title":"A statistical model to correct systematic bias introduced by algorithmic thresholds in protein structural comparison algorithms","author":"Fofanov","year":"2008","journal-title":"Bioinf. Biomed. Workshops"},{"key":"2023020110450069900_btv637-B5","doi-asserted-by":"crossref","first-page":"D485","DOI":"10.1093\/nar\/gkt1243","article-title":"The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes","volume":"42","author":"Furnham","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023020110450069900_btv637-B6","doi-asserted-by":"crossref","first-page":"4501","DOI":"10.1021\/cr000033x","article-title":"Serine protease mechanism and specificity","volume":"102","author":"Hedstrom","year":"2002","journal-title":"Chem. Rev."},{"key":"2023020110450069900_btv637-B7","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1089\/cmb.2014.0263","article-title":"A novel algorithm for enhanced structural motif matching in proteins","volume":"22","author":"Kaiser","year":"2015","journal-title":"J. Comput. Biol."},{"key":"2023020110450069900_btv637-B8","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1016\/j.str.2012.09.006","article-title":"Host-pathogen crosstalking: the mastery of taking the helm of the host","volume":"20","author":"Koutsotoli","year":"2012","journal-title":"Structure"},{"key":"2023020110450069900_btv637-B9","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1002\/prot.20099","article-title":"Superfamily active site templates","volume":"55","author":"Meng","year":"2004","journal-title":"Proteins"},{"key":"2023020110450069900_btv637-B10","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1093\/bioinformatics\/btu769","article-title":"Achievements and challenges in structural bioinformatics and computational biophysics","volume":"31","author":"Samish","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020110450069900_btv637-B11","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1016\/S0022-2836(03)00045-7","article-title":"A model for statistical significance of local similarities in structure","volume":"326","author":"Stark","year":"2003","journal-title":"J. Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/5\/792\/49017668\/bioinformatics_32_5_792.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/5\/792\/49017668\/bioinformatics_32_5_792.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:01:20Z","timestamp":1675288880000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/5\/792\/1744023"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,10,30]]},"references-count":11,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2016,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv637","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,3,1]]},"published":{"date-parts":[[2015,10,30]]}}}