{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T23:28:43Z","timestamp":1772148523568,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":351,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: \u00a0Omokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB). The server compares global shapes of assemblies independent of sequence order and number of subunits. As a search query, the user inputs a structure ID (PDB ID or EMDB ID) or uploads an atomic model or 3D density map to the server. The search is performed usually within 1\u2009min, using one-dimensional profiles (incremental distance rank profiles) to characterize the shapes. Using the gmfit (Gaussian mixture model fitting) program, the found structures are fitted onto the query structure and their superimposed structures are displayed on the Web browser. Our service provides new structural perspectives to life science researchers.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0Omokage search is freely accessible at http:\/\/pdbj.org\/omokage\/.<\/jats:p>\n               <jats:p>Contact: \u00a0hirofumi@protein.osaka-u.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv614","type":"journal-article","created":{"date-parts":[[2015,10,28]],"date-time":"2015-10-28T02:38:45Z","timestamp":1445999925000},"page":"619-620","source":"Crossref","is-referenced-by-count":42,"title":["Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB"],"prefix":"10.1093","volume":"32","author":[{"given":"Hirofumi","family":"Suzuki","sequence":"first","affiliation":[{"name":"Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takeshi","family":"Kawabata","sequence":"additional","affiliation":[{"name":"Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haruki","family":"Nakamura","sequence":"additional","affiliation":[{"name":"Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,27]]},"reference":[{"key":"2023020110351547400_btv614-B1","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkl971","article-title":"The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data","volume":"35","author":"Berman","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023020110351547400_btv614-B2","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1186\/s12859-015-0580-6","article-title":"Navigating 3D electron microscopy maps with EM-SURFER","volume":"16","author":"Esquivel-Rodriguez","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2023020110351547400_btv614-B3","doi-asserted-by":"crossref","first-page":"4643","DOI":"10.1529\/biophysj.108.137125","article-title":"Multiple subunit fitting into a low-resolution density map of a macromolecular complex using Gaussian mixture model","volume":"95","author":"Kawabata","year":"2008","journal-title":"Biophys.J."},{"key":"2023020110351547400_btv614-B4","doi-asserted-by":"crossref","first-page":"D453","DOI":"10.1093\/nar\/gkr811","article-title":"Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format","volume":"40","author":"Kinjo","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020110351547400_btv614-B5","doi-asserted-by":"crossref","first-page":"D456","DOI":"10.1093\/nar\/gkq880","article-title":"EMDataBank.org: unified data resource for CryoEM","volume":"39","author":"Lawson","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023020110351547400_btv614-B6","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1126\/science.270.5241.1464","article-title":"Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog","volume":"5241","author":"Nissen","year":"1995","journal-title":"Science"},{"key":"2023020110351547400_btv614-B7","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1006\/jmbi.1998.2232","article-title":"Self-organizing neural networks bridge the biomolecular resolution gap","volume":"284","author":"Wriggers","year":"1998","journal-title":"J. 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