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direct coupling analysis of residue coevolution captures native contacts

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How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins? Direct coupling analysis for protein contact prediction. Quantitative Biology - Quantitative Methods; Condensed Matter - Statistical Mechanics. Crucial to this inference is the ability to disentangle direct and indirect correlations, as accomplished by the recently introduced direct-coupling analysis (DCA). Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Agreement NNX16AC86A, Proceedings of the National Academy of Science, Is ADS down? Our findings suggest that contacts predicted by DCA can be used as a reliable guide to facilitate computational predictions of alternative protein conformations, protein complex formation, and even the de novo prediction of protein domain structures, contingent on the existence of a large number of homologous sequences which are being rapidly made available due to advances in genome sequencing. You are currently offline. The basic hypothesis connecting correlated substitution pat- terns and residue–residue contacts is very simple: If two residues of a protein or a pair of interacting proteins form a contact, a destabilizing amino acid substitution at one position is expected tobecompensatedbyasubstitutionoftheotherpositionoverthe evolutionary timescale, in order for the residue pair to maintain attractive interaction. Use, Smithsonian Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments, On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model, Determination of network of residues that regulate allostery in protein families using sequence analysis, Identification of direct residue contacts in protein–protein interaction by message passing, Correlated mutations and residue contacts in proteins. It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the tertiary protein structure. It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the tertiary protein structure. Furthermore, our analysis captures clear signals beyond intradomain residue contacts, arising, e.g., from alternative protein conformations, ligand-mediated residue couplings, and interdomain interactions in protein oligomers. Some features of the site may not work correctly. Faruck Morcos Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0374, USA. Crucial to this inference is the ability to disentangle direct and indirect correlations, as accomplished by the recently introduced direct-coupling analysis (DCA…. It has long been suggested that the resulting correlations among amino acid compositions at different sequence positions can be exploited to infer spatial contacts within the … Direct-coupling analysis of residue coevolution captures native contacts across many protein families Faruck Morcos, Andrea Pagnani, Bryan Lunt, Arianna Bertolino, Debora S. Marks, Chris Sander, Riccardo Zecchina, José N. Onuchic, Terence Hwa, and Martin Weigt PNAS December 6, 2011 108 (49) E1293-E1301; https://doi.org/10.1073/pnas.1111471108 3D Protein Structure Predicted from Sequence, Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction, Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments, Blog posts, news articles and tweet counts and IDs sourced by, Proceedings of the National Academy of Sciences, View 5 excerpts, cites background and methods, Protein science : a publication of the Protein Society, By clicking accept or continuing to use the site, you agree to the terms outlined in our, A Fundamental Breakthrough in Protein Folding. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. The ADS is operated by the Smithsonian Astrophysical Observatory under NASA Cooperative Semantic Scholar is a free, AI-powered research tool for scientific literature, based at the Allen Institute for AI. Here we develop a computationally efficient implementation of DCA, which allows us to evaluate the accuracy of contact prediction by DCA for a large number of protein domains, based purely on sequence information. Supplementary text: Direct-coupling analysis of residue co-evolution captures native contacts across many protein families F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. Marks, C. Sander, R. Zecchina, J.N. Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis, Statistical investigations of protein residue direct couplings, Evolutionary couplings detect side-chain interactions, From residue coevolution to protein conformational ensembles and functional dynamics, Patterns of coevolving amino acids unveil structural and dynamical domains. Notice, Smithsonian Terms of (or is it just me...), Smithsonian Privacy Astrophysical Observatory. DCA is shown to yield a large number of correctly predicted contacts, recapitulating the global structure of the contact map for the majority of the protein domains examined.

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November 13, 2020 |

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