{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T16:27:20Z","timestamp":1762100840953},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2887,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present a large-scale implementation of the Rankprop protein homology ranking algorithm in the form of an openly accessible web server. We use the NRDB40 PSI-BLAST all-versus-all protein similarity network of 1.1 million proteins to construct the graph for the Rankprop algorithm, whereas previously, results were only reported for a database of 108 000 proteins. We also describe two algorithmic improvements to the original algorithm, including propagation from multiple homologs of the query and better normalization of ranking scores, that lead to higher accuracy and to scores with a probabilistic interpretation.<\/jats:p>\n               <jats:p>Availability: The Rankprop web server and source code are available at http:\/\/rankprop.gs.washington.edu<\/jats:p>\n               <jats:p>Contact: \u00a0iain@nec-labs.com; noble@gs.washington.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn567","type":"journal-article","created":{"date-parts":[[2008,11,7]],"date-time":"2008-11-07T01:24:14Z","timestamp":1226021054000},"page":"121-122","source":"Crossref","is-referenced-by-count":20,"title":["R<scp>ankprop<\/scp>: a web server for protein remote homology detection"],"prefix":"10.1093","volume":"25","author":[{"given":"Iain","family":"Melvin","sequence":"first","affiliation":[{"name":"1 NEC Laboratories of America, Princeton, NJ, 2Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, 3Department of Genome Sciences and 4Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"}]},{"given":"Jason","family":"Weston","sequence":"additional","affiliation":[{"name":"1 NEC Laboratories of America, Princeton, NJ, 2Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, 3Department of Genome Sciences and 4Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"}]},{"given":"Christina","family":"Leslie","sequence":"additional","affiliation":[{"name":"1 NEC Laboratories of America, Princeton, NJ, 2Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, 3Department of Genome Sciences and 4Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"}]},{"given":"William Stafford","family":"Noble","sequence":"additional","affiliation":[{"name":"1 NEC Laboratories of America, Princeton, NJ, 2Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, 3Department of Genome Sciences and 4Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"},{"name":"1 NEC Laboratories of America, Princeton, NJ, 2Computational Biology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, 3Department of Genome Sciences and 4Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA"}]}],"member":"286","published-online":{"date-parts":[[2008,11,6]]},"reference":[{"key":"2023013110030083800_B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023013110030083800_B2","doi-asserted-by":"crossref","first-page":"D276","DOI":"10.1093\/nar\/gkm879","article-title":"Pairsdb atlas of protein sequence space","volume":"36","author":"Heger","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013110030083800_B3","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: a structural classification of proteins database for the investigation of sequences and structures","volume":"247","author":"Murzin","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2023013110030083800_B4","doi-asserted-by":"crossref","first-page":"6559","DOI":"10.1073\/pnas.0308067101","article-title":"Protein ranking: from local to global structure in the protein similarity network","volume":"101","author":"Weston","year":"2004","journal-title":"Proc. Natl Acad. Sci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/1\/121\/48982686\/bioinformatics_25_1_121.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/1\/121\/48982686\/bioinformatics_25_1_121.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:26:26Z","timestamp":1675189586000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/1\/121\/301699"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,11,6]]},"references-count":4,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn567","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,1,1]]},"published":{"date-parts":[[2008,11,6]]}}}