{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T21:13:42Z","timestamp":1717708422698},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Graphical representations of proteins in online databases generally give default views orthogonal to the PDB file coordinate system. These views are often uninformative in terms of protein structure and\/or function. Here we discuss the development of a simple automatic algorithm to provide a \u2018good\u2019 view of a protein domain with respect to its structural features.<\/jats:p>\n               <jats:p>Results: We used dimension reduction with the preservation of topology (using Kohonen\u2019s self organising map) to map 3D carbon alpha coordinates into 2D. The original protein structure was then rotated to the view which corresponded most closely to the 2D mapping. This procedure, which we call OVOP, was evaluated in a public blind trial on the web against random views and a \u2018flattest\u2019 view. The OVOP views were consistently rated \u2018better\u2019 than the other views by our volunteers.<\/jats:p>\n               <jats:p>Availability: The source code is available from the OVOP homepage: http:\/\/www.sbc.su.se\/~oscar\/ovop<\/jats:p>\n               <jats:p>Contact: maccallr@sbc.su.se<\/jats:p>\n               <jats:p>* To whom correspondence should be addressed.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg100","type":"journal-article","created":{"date-parts":[[2003,4,30]],"date-time":"2003-04-30T19:43:50Z","timestamp":1051731830000},"page":"882-888","source":"Crossref","is-referenced-by-count":2,"title":["Towards optimal views of proteins"],"prefix":"10.1093","volume":"19","author":[{"given":"Oscar","family":"Sverud","sequence":"first","affiliation":[{"name":"Stockholm Bioinformatics Center, Stockholm University, 106 91 Stockholm, Sweden"}]},{"given":"Robert M.","family":"MacCallum","sequence":"additional","affiliation":[{"name":"Stockholm Bioinformatics Center, Stockholm University, 106 91 Stockholm, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2003,5,1]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/19\/7\/882\/48904335\/bioinformatics_19_7_882.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/19\/7\/882\/48904335\/bioinformatics_19_7_882.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T17:23:43Z","timestamp":1674667423000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/7\/882\/197662"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,5,1]]},"references-count":0,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2003,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg100","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2003,5,1]]},"published":{"date-parts":[[2003,5,1]]}}}