{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T13:19:29Z","timestamp":1758892769011},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2002,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Many of the most interesting functional and evolutionary relationships among proteins are so ancient that they cannot be reliably detected through sequence analysis and are apparent only through a comparison of the tertiary structures. The conserved features can often be described as structural motifs consisting of a few single residues or Secondary Structure (SS) elements. Confidence in such motifs is greatly boosted when they are found in more than a pair of proteins.<\/jats:p>\n               <jats:p>Results: We describe an algorithm for the automatic discovery of recurring patterns in protein structures. The patterns consist of individual residues having a defined order along the protein\u2019s backbone that come close together in the structure and whose spatial conformations are similar. The residues in a pattern need not be close in the protein\u2019s sequence. The work described in this paper builds on an earlier reported algorithm for motif discovery. This paper describes a significant improvement of the algorithm which makes it very efficient. The improved efficiency allows us to use it for doing unsupervised learning of patterns occurring in small subsets in a large set of structures, a non-redundant subset of the Protein Data Bank (PDB) database of all known protein structures.<\/jats:p>\n               <jats:p>Availability: The program is freely available to academia, requests can be sent to Inge.Jonassen@ii.uib.no.<\/jats:p>\n               <jats:p>Contact: Inge.Jonassen@ii.uib.no<\/jats:p>\n               <jats:p>* To whom correspondence should be addressed.<\/jats:p>","DOI":"10.1093\/bioinformatics\/18.2.362","type":"journal-article","created":{"date-parts":[[2002,7,26]],"date-time":"2002-07-26T22:37:51Z","timestamp":1027723071000},"page":"362-367","source":"Crossref","is-referenced-by-count":29,"title":["Structure motif discovery and mining the PDB"],"prefix":"10.1093","volume":"18","author":[{"given":"Inge","family":"Jonassen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ingvar","family":"Eidhammer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darrell","family":"Conklin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William R.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2002,2,1]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/18\/2\/362\/48850516\/bioinformatics_18_2_362.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/18\/2\/362\/48850516\/bioinformatics_18_2_362.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:24:55Z","timestamp":1674631495000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/18\/2\/362\/225853"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2002,2,1]]},"references-count":0,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2002,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/18.2.362","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2002,2]]},"published":{"date-parts":[[2002,2,1]]}}}