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PSICOV: precisestructural contactprediction usingsparse inversecovariance estimationon large multiplesequence alignments David T. JonesDaniel BuchanDomenico Cozzetto2011 год

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
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Аннотация: Abstract Motivation: The accurate prediction of residue–residue contacts, critical for maintaining the native fold of a protein, remains an open problem in the field of structural bioinformatics. Interest in this long-standing problem has increased recently with algorithmic improvements and the rapid growth in the sizes of sequence families. Progress could have major impacts in both structure and function prediction to name but two benefits. Sequence-based contact predictions are usually made by identifying correlated mutations within multiple sequence alignments (MSAs), most commonly through the information-theoretic approach of calculating mutual information between pairs of sites in proteins. These predictions are often inaccurate because the true covariation signal in the MSA is often masked by biases from many ancillary indirect-coupling or phylogenetic effects. Here we present a novel method, PSICOV, which introduces the use of sparse inverse covariance estimation to the problem of protein contact prediction. Our method builds on work which had previously demonstrated corrections for phylogenetic and entropic correlation noise and allows accurate discrimination of direct from indirectly coupled mutation correlations in the MSA. Results: PSICOV displays a mean precision substantially better than the best performing normalized mutual information approach and Bayesian networks. For 118 out of 150 targets, the L/5 (i.e. top-L/5 predictions for a protein of length L) precision for long-range contacts (sequence separation >23) was ≥0.5, which represents an improvement sufficient to be of significant benefit in protein structure prediction or model quality assessment. Availability: The PSICOV source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/PSICOV Contact: d.jones@cs.ucl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Год издания: 2011
Авторы: David T. Jones, Daniel Buchan, Domenico Cozzetto, Massimiliano Pontil
Издательство: Oxford University Press
Источник: Bioinformatics
Ключевые слова: Genomics and Phylogenetic Studies, Machine Learning in Bioinformatics, Protein Structure and Dynamics
Другие ссылки: Bioinformatics (PDF)
Bioinformatics (HTML)
PubMed (HTML)