| Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution. | |
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MedLine Citation:
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PMID: 20529918 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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MOTIVATION: One of the most successful methods to date for recognizing protein sequences that are evolutionarily related, has been profile hidden Markov models. However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in beta-sheets. We thus explore methods for incorporating pairwise dependencies into these models. RESULTS: We consider the remote homology detection problem for beta-structural motifs. In particular, we ask if a statistical model trained on members of only one family in a SCOP beta-structural superfamily, can recognize members of other families in that superfamily. We show that HMMs trained with our pairwise model of simulated evolution achieve nearly a median 5% improvement in AUC for beta-structural motif recognition as compared to ordinary HMMs. AVAILABILITY: All datasets and HMMs are available at: http://bcb.cs.tufts.edu/pairwise/. |
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Authors:
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Anoop Kumar; Lenore Cowen |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: 26 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2010 Jun |
Date Detail:
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Created Date: 2010-06-09 Completed Date: 2010-10-21 Revised Date: 2013-05-29 |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: England |
Other Details:
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Languages: eng Pagination: i287-93 Citation Subset: IM |
Affiliation:
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Department of Computer Science, Tufts University, Medford, MA, USA. anoop.kumar@tufts.edu |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Amino Acid Motifs* Evolution, Molecular* Hydrogen Bonding Markov Chains Protein Structure, Tertiary Proteins / chemistry* |
| Grant Support | |
ID/Acronym/Agency:
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1R01GM080330-01A1/GM/NIGMS NIH HHS; R01 GM080330-01A1/GM/NIGMS NIH HHS; R01 GM080330-04/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Proteins |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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