{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T20:15:33Z","timestamp":1722716133018},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2017,1,27]],"date-time":"2017-01-27T00:00:00Z","timestamp":1485475200000},"content-version":"vor","delay-in-days":1078,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,6,15]]},"abstract":"<jats:p>Motivation: fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project.<\/jats:p>\n               <jats:p>Results: fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60\u00d7 faster than qcprot and 3\u00d7 faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250\u00d7 and 2000\u00d7 faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco.<\/jats:p>\n               <jats:p>Availability and implementation: fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license. (http:\/\/software.compbio.washington.edu\/fast_protein_cluster)<\/jats:p>\n               <jats:p>Contact: \u00a0lhhung@compbio.washington.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu098","type":"journal-article","created":{"date-parts":[[2014,2,15]],"date-time":"2014-02-15T02:04:22Z","timestamp":1392429862000},"page":"1774-1776","source":"Crossref","is-referenced-by-count":13,"title":["fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data"],"prefix":"10.1093","volume":"30","author":[{"given":"Ling-Hong","family":"Hung","sequence":"first","affiliation":[{"name":"1Department of Microbiology, University of Washington, Seattle, WA 98109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ram","family":"Samudrala","sequence":"additional","affiliation":[{"name":"1Department of Microbiology, University of Washington, Seattle, WA 98109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,2,14]]},"reference":[{"key":"2023012711015447300_btu098-B1","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1093\/bioinformatics\/bts345","article-title":"Accelerated protein structure comparison using TM-score-GPU","volume":"28","author":"Hung","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711015447300_btu098-B3","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/1471-2105-14-62","article-title":"ClusCo: clustering and comparison of protein models","volume":"14","author":"Jamroz","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023012711015447300_btu098-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v053.i09","article-title":"fastcluster: Fast hierarchical, agglomerative clustering routines for R and Python","volume":"53","author":"M\u00fcllner","year":"2013","journal-title":"J. Stat. Softw."},{"key":"2023012711015447300_btu098-B6","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1107\/S0108767305015266","article-title":"Rapid calculation of RMSDs using a quaternion-based characteristic polynomial","volume":"61","author":"Theobald","year":"2005","journal-title":"Acta Crystallogr. A"},{"key":"2023012711015447300_btu098-B8","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1002\/jcc.20011","article-title":"SPICKER: a clustering approach to identify near-native protein folds","volume":"25","author":"Zhang","year":"2004","journal-title":"J. Comput. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/12\/1774\/48924131\/bioinformatics_30_12_1774.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/12\/1774\/48924131\/bioinformatics_30_12_1774.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:02:32Z","timestamp":1674817352000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/12\/1774\/2748135"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,2,14]]},"references-count":5,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2014,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu098","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2014,6,15]]},"published":{"date-parts":[[2014,2,14]]}}}