{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T20:50:40Z","timestamp":1784235040744,"version":"3.55.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2928,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Red Queen said, \u2018It takes all the running you can do, to keep in the same place.\u2019 Lewis Carrol<\/jats:p>\n               <jats:p>Motivation: Newly solved protein structures are routinely scanned against structures already in the Protein Data Bank (PDB) using Internet servers. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The number of known structures continues to grow exponentially. Sensitive\u2014thorough but slow\u2014search algorithms are challenged to deliver results in a reasonable time, as there are now more structures in the PDB than seconds in a day. The brute-force solution would be to distribute the individual comparisons on a massively parallel computer. A frugal solution, as implemented in the Dali server, is to reduce the total computational cost by pruning search space using prior knowledge about the distribution of structures in fold space. This note reports paradigm revisions that enable maintaining such a knowledge base up-to-date on a PC.<\/jats:p>\n               <jats:p>Availability: The Dali server for protein structure database searching at http:\/\/ekhidna.biocenter.helsinki.fi\/dali_server is running DaliLite v.3. The software can be downloaded for academic use from http:\/\/ekhidna.biocenter.helsinki.fi\/dali_lite\/downloads\/v3.<\/jats:p>\n               <jats:p>Contact: \u00a0liisa.holm@helsinki.fi<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn507","type":"journal-article","created":{"date-parts":[[2008,9,26]],"date-time":"2008-09-26T00:13:43Z","timestamp":1222388023000},"page":"2780-2781","source":"Crossref","is-referenced-by-count":907,"title":["Searching protein structure databases with DaliLite v.3"],"prefix":"10.1093","volume":"24","author":[{"given":"L.","family":"Holm","sequence":"first","affiliation":[{"name":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"},{"name":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"K\u00e4\u00e4ri\u00e4inen","sequence":"additional","affiliation":[{"name":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P.","family":"Rosenstr\u00f6m","sequence":"additional","affiliation":[{"name":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Schenkel","sequence":"additional","affiliation":[{"name":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,9,25]]},"reference":[{"key":"2023020212234187600_B1","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1093\/bioinformatics\/btm358","article-title":"The global trace graph, a novel paradigm for searching protein sequence databases","volume":"23","author":"Heger","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020212234187600_B2","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1093\/bioinformatics\/16.6.566","article-title":"DaliLite workbench for protein structure comparison","volume":"16","author":"Holm","year":"2000","journal-title":"Bioinformatics"},{"key":"2023020212234187600_B3","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1002\/prot.340190302","article-title":"Searching protein structure databases has come of age","volume":"19","author":"Holm","year":"1994","journal-title":"Proteins"},{"key":"2023020212234187600_B4","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020212234187600_B5","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. 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