{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T18:34:34Z","timestamp":1769020474412,"version":"3.49.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:The widespread coiled-coil structural motif in proteins is known to mediate a variety of biological interactions. Recognizing a coiled-coil containing sequence and locating its coiled-coil domains are key steps towards the determination of the protein structure and function. Different tools are available for predicting coiled-coil domains in protein sequences, including those based on position-specific score matrices and machine learning methods.<\/jats:p>\n               <jats:p>Results: In this article, we introduce a hidden Markov model (CCHMM_PROF) that exploits the information contained in multiple sequence alignments (profiles) to predict coiled-coil regions. The new method discriminates coiled-coil sequences with an accuracy of 97% and achieves a true positive rate of 79% with only 1% of false positives. Furthermore, when predicting the location of coiled-coil segments in protein sequences, the method reaches an accuracy of 80% at the residue level and a best per-segment and per-protein efficiency of 81% and 80%, respectively. The results indicate that CCHMM_PROF outperforms all the existing tools and can be adopted for large-scale genome annotation.<\/jats:p>\n               <jats:p>Availability: The dataset is available at http:\/\/www.biocomp.unibo.it\/\u223clisa\/coiled-coils. The predictor is freely available at http:\/\/gpcr.biocomp.unibo.it\/cgi\/predictors\/cchmmprof\/pred_cchmmprof.cgi.<\/jats:p>\n               <jats:p>Contact: \u00a0piero@biocomp.unibo.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp539","type":"journal-article","created":{"date-parts":[[2009,9,11]],"date-time":"2009-09-11T00:34:34Z","timestamp":1252629274000},"page":"2757-2763","source":"Crossref","is-referenced-by-count":47,"title":["CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information"],"prefix":"10.1093","volume":"25","author":[{"given":"Lisa","family":"Bartoli","sequence":"first","affiliation":[{"name":"1 Biocomputing Group, Department of Biology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy and 2 The Bioinformatics Center, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, 2200 Copenhagen, Denmark"}]},{"given":"Piero","family":"Fariselli","sequence":"additional","affiliation":[{"name":"1 Biocomputing Group, Department of Biology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy and 2 The Bioinformatics Center, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, 2200 Copenhagen, Denmark"}]},{"given":"Anders","family":"Krogh","sequence":"additional","affiliation":[{"name":"1 Biocomputing Group, Department of Biology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy and 2 The Bioinformatics Center, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, 2200 Copenhagen, Denmark"}]},{"given":"Rita","family":"Casadio","sequence":"additional","affiliation":[{"name":"1 Biocomputing Group, Department of Biology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy and 2 The Bioinformatics Center, Department of Biology, University of Copenhagen, Ole Maal\u00f8es Vej 5, 2200 Copenhagen, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2009,9,10]]},"reference":[{"key":"2023013112175751400_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":"2023013112175751400_B2","doi-asserted-by":"crossref","first-page":"8259","DOI":"10.1073\/pnas.92.18.8259","article-title":"Predicting coiled coils by use of pairwise residue correlations","volume":"92","author":"Berger","year":"1995","journal-title":"Proc. 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