{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T10:39:45Z","timestamp":1774262385231,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Contact maps are a convenient method for the structural biologists to identify structural features through two-dimensional simplification. Binary (yes\/no) contact maps with a single cutoff distance can be generalized to show continuous distance ranges. We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. binding-site residues) and global (e.g. hinge motion), between unbound and bound proteins through distance patterns. Users can target residue pairs in RRDistMaps for further navigation in Chimera. The interface contains the unique features of identifying long-range residue motion and aligning sequences to simultaneously compare distance maps.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0RRDistMaps was developed as part of UCSF Chimera release 1.10, which is freely available at http:\/\/rbvi.ucsf.edu\/chimera\/download.html, and operates on Linux, Windows, and Mac OS.<\/jats:p>\n               <jats:p>Contact: \u00a0conrad@cgl.ucsf.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu841","type":"journal-article","created":{"date-parts":[[2014,12,25]],"date-time":"2014-12-25T04:16:00Z","timestamp":1419480960000},"page":"1484-1486","source":"Crossref","is-referenced-by-count":69,"title":["RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps"],"prefix":"10.1093","volume":"31","author":[{"given":"Jonathan E.","family":"Chen","sequence":"first","affiliation":[{"name":"1 Lowell High School, San Francisco, CA and 2Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA, USA"}]},{"given":"Conrad C.","family":"Huang","sequence":"additional","affiliation":[{"name":"1 Lowell High School, San Francisco, CA and 2Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA, USA"}]},{"given":"Thomas E.","family":"Ferrin","sequence":"additional","affiliation":[{"name":"1 Lowell High School, San Francisco, CA and 2Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,12,24]]},"reference":[{"key":"2023051308500275400_btu841-B1","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023051308500275400_btu841-B2","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1006\/jmbi.1993.1489","article-title":"Protein structure comparison by alignment of distance matrices","volume":"233","author":"Holm","year":"1993","journal-title":"J. Mol. Biol."},{"key":"2023051308500275400_btu841-B3","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1093\/nar\/gku377","article-title":"Enhancing UCSF Chimera through web services","volume":"42","author":"Huang","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023051308500275400_btu841-B4","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the ammo acid sequence of two proteins","volume":"48","author":"Needleman","year":"1970","journal-title":"J. Mol. Biol."},{"key":"2023051308500275400_btu841-B5","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"2023051308500275400_btu841-B6","doi-asserted-by":"crossref","first-page":"1573","DOI":"10.1093\/bioinformatics\/btr163","article-title":"CMView: interactive contact map visualization and analysis","volume":"27","author":"Vehlow","year":"2011","journal-title":"Bioinformatics"},{"key":"2023051308500275400_btu841-B7","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1093\/bioinformatics\/btn069","article-title":"A comprehensive assessment of sequence-based and template-based methods for protein contact prediction","volume":"24","author":"Wu","year":"2008","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/9\/1484\/50306423\/bioinformatics_31_9_1484.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/9\/1484\/50306423\/bioinformatics_31_9_1484.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T08:50:19Z","timestamp":1683967819000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/9\/1484\/200426"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12,24]]},"references-count":7,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2015,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu841","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,5,1]]},"published":{"date-parts":[[2014,12,24]]}}}