{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T14:57:34Z","timestamp":1767193054077},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003,3,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Existing algorithms for automated protein structure alignment generate contradictory results and are difficult to interpret. An algorithm which can provide a context for interpreting the alignment and uses a simple method to characterize protein structure similarity is needed.<\/jats:p>\n               <jats:p>Results: We describe a heuristic for limiting the search space for structure alignment comparisons between two proteins, and an algorithm for finding minimal root-mean-squared-distance (RMSD) alignments as a function of the number of matching residue pairs within this limited search space. Our alignment algorithm uses coordinates of alpha-carbon atoms to represent each amino acid residue and requires a total computation time of O(m3n2), where m and n denote the lengths of the protein sequences. This makes our method fast enough for comparisons of moderate-size proteins (fewer than \u223c800 residues) on current workstation-class computers and therefore addresses the need for a systematic analysis of multiple plausible shape similarities between two proteins using a widely accepted comparison metric.<\/jats:p>\n               <jats:p>Availability: See http:\/\/www.cgl.ucsf.edu\/Research\/minrms<\/jats:p>\n               <jats:p>Contact: tef@cgl.ucsf.edu<\/jats:p>\n               <jats:p>* To whom correspondence should be addressed.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg035","type":"journal-article","created":{"date-parts":[[2003,3,21]],"date-time":"2003-03-21T19:31:39Z","timestamp":1048275099000},"page":"625-634","source":"Crossref","is-referenced-by-count":44,"title":["MINRMS: an efficient algorithm for determining protein structure\nsimilarity using root-mean-squared-distance"],"prefix":"10.1093","volume":"19","author":[{"given":"Andrew I.","family":"Jewett","sequence":"first","affiliation":[{"name":"Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA"}]},{"given":"Conrad C.","family":"Huang","sequence":"additional","affiliation":[{"name":"Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA"}]},{"given":"Thomas E.","family":"Ferrin","sequence":"additional","affiliation":[{"name":"Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446 USA"}]}],"member":"286","published-online":{"date-parts":[[2003,3,22]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/19\/5\/625\/48904120\/bioinformatics_19_5_625.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/19\/5\/625\/48904120\/bioinformatics_19_5_625.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T16:44:57Z","timestamp":1674665097000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/5\/625\/239328"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,3,22]]},"references-count":0,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2003,3,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg035","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2003,3,22]]},"published":{"date-parts":[[2003,3,22]]}}}