{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:33:05Z","timestamp":1732033985607},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Over the last decade, both static and dynamic fragment libraries for protein structure prediction have been introduced. The former are built from clusters in either sequence or structure space and aim to extract a universal structural alphabet. The latter are tailored for a particular query protein sequence and aim to provide local structural templates that need to be assembled in order to build the full-length structure.<\/jats:p>\n               <jats:p>Results: Here, we introduce HHfrag, a dynamic HMM-based fragment search method built on the profile\u2013profile comparison tool HHpred. We show that HHfrag provides advantages over existing fragment assignment methods in that it: (i) improves the precision of the fragments at the expense of a minor loss in sequence coverage; (ii) detects fragments of variable length (6\u201321 amino acid residues); (iii) allows for gapped fragments and (iv) does not assign fragments to regions where there is no clear sequence conservation. We illustrate the usefulness of fragments detected by HHfrag on targets from most recent CASP.<\/jats:p>\n               <jats:p>Availability: A web server for running HHfrag is available at http:\/\/toolkit.tuebingen.mpg.de\/hhfrag. The source code is available at http:\/\/www.eb.tuebingen.mpg.de\/departments\/1-protein-evolution\/michael-habeck\/HHfrag.tar.gz<\/jats:p>\n               <jats:p>Contact: \u00a0michael.habeck@tuebingen.mpg.de<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr541","type":"journal-article","created":{"date-parts":[[2011,9,30]],"date-time":"2011-09-30T10:29:20Z","timestamp":1317378560000},"page":"3110-3116","source":"Crossref","is-referenced-by-count":28,"title":["HHfrag: HMM-based fragment detection using HHpred"],"prefix":"10.1093","volume":"27","author":[{"given":"Ivan","family":"Kalev","sequence":"first","affiliation":[{"name":"1 Department of Protein Evolution and 2Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Spemannstrasse 38, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Habeck","sequence":"additional","affiliation":[{"name":"1 Department of Protein Evolution and 2Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Spemannstrasse 38, 72076 T\u00fcbingen, Germany"},{"name":"1 Department of Protein Evolution and 2Department of Empirical Inference, Max Planck Institute for Intelligent Systems, Spemannstrasse 38, 72076 T\u00fcbingen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,9,28]]},"reference":[{"key":"2023012511320748300_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":"2023012511320748300_B2","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.sbi.2008.02.006","article-title":"Cradle-loop barrels and the concept of metafolds in protein classification by natural descent","volume":"18","author":"Alva","year":"2008","journal-title":"Curr. 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