{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T14:04:42Z","timestamp":1761487482813},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The prediction of protein domains is a crucial task for functional classification, homology-based structure prediction and structural genomics. In this paper, we present the SSEP-Domain protein domain prediction approach, which is based on the application of secondary structure element alignment (SSEA) and profile\u2013profile alignment (PPA) in combination with InterPro pattern searches. SSEA allows rapid screening for potential domain regions while PPA provides us with the necessary specificity for selecting significant hits. The combination with InterPro patterns allows finding domain regions without solved structural templates if sequence family definitions exist.<\/jats:p>\n               <jats:p>Results: A preliminary version of SSEP-Domain was ranked among the top-performing domain prediction servers in the CASP 6 and CAFASP 4 experiments. Evaluation of the final version shows further improvement over these results together with a significant speed-up.<\/jats:p>\n               <jats:p>Availability: The server is available at<\/jats:p>\n               <jats:p>Contact: \u00a0jan.gewehr@bio.ifi.lmu.de<\/jats:p>\n               <jats:p>Supplementary information: The supplementary data are available at<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti751","type":"journal-article","created":{"date-parts":[[2005,11,3]],"date-time":"2005-11-03T01:13:48Z","timestamp":1130980428000},"page":"181-187","source":"Crossref","is-referenced-by-count":41,"title":["SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles"],"prefix":"10.1093","volume":"22","author":[{"given":"Jan E.","family":"Gewehr","sequence":"first","affiliation":[{"name":"Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University \u00a0 Amalienstrasse 17, D-80333 Munich, Germany"}]},{"given":"Ralf","family":"Zimmer","sequence":"additional","affiliation":[{"name":"Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University \u00a0 Amalienstrasse 17, D-80333 Munich, Germany"}]}],"member":"286","published-online":{"date-parts":[[2005,11,2]]},"reference":[{"key":"2023012408312854700_b1","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012408312854700_b2","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1093\/protein\/gzg106","article-title":"MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification","volume":"16","author":"Bindewald","year":"2003","journal-title":"Protein Eng."},{"key":"2023012408312854700_b3","doi-asserted-by":"crossref","first-page":"D189","DOI":"10.1093\/nar\/gkh034","article-title":"The ASTRAL compendium in 2004","volume":"32","author":"Chandonia","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012408312854700_b4","article-title":"DOMpro: protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neutral networks","author":"Cheng","year":"2005","journal-title":"Data Mining Knowl. 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