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  bbcontacts: Prediction of β-strand pairing from direct coupling patterns.

Andreani, J., & Söding, J. (2015). bbcontacts: Prediction of β-strand pairing from direct coupling patterns. Bioinformatics, 31(11), 1729-1737. doi:10.1093/bioinformatics/btv041.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0024-AE80-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0029-61A9-E
Genre: Journal Article

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Andreani, J.1, Author              
Söding, J.1, Author              
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1Research Group of Computational Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_1933286              

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 Abstract: Motivation: It has recently become possible to build reliable de novo models of proteins if a multiple sequence alignment (MSA) of at least 1000 homologous sequences can be built. Methods of global statistical network analysis can explain the observed correlations between columns in the MSA by a small set of directly coupled pairs of columns. Strong couplings are indicative of residue-residue contacts, and from the predicted contacts a structure can be computed. Here, we exploit the structural regularity of paired β-strands that leads to characteristic patterns in the noisy matrices of couplings. The β-β contacts should be detected more reliably than single contacts, reducing the required number of sequences in the MSAs. Results: bbcontacts predicts β-β contacts by detecting these characteristic patterns in the 2D map of coupling scores using two hidden Markov models (HMMs), one for parallel and one for antiparallel contacts. β-bulges are modeled as indel states. In contrast to existing methods, bbcontacts uses predicted instead of true secondary structure. On a standard set of 916 test proteins, 34% of which have MSAs with <1000 sequences, bbcontacts achieves 50% precision for contacting β-β residue pairs at 50% recall using predicted secondary structure and 64% precision at 64% recall using true secondary structure, while existing tools achieve around 45% precision at 45% recall using true secondary structure. Availability: bbcontacts is open source software (GNU Affero GPL v3) available at https://bitbucket.org/soedinglab/bbcontacts

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Language(s): eng - English
 Dates: 2015-01-23
 Publication Status: Published online
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 Rev. Method: Peer
 Identifiers: DOI: 10.1093/bioinformatics/btv041
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Title: Bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 31 (11) Sequence Number: - Start / End Page: 1729 - 1737 Identifier: -