Statistical Investigations of Protein Residue Direct Couplings, Direct coevolutionary couplings reflect biophysical residue interactions in proteins. Notice, Smithsonian Terms of Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Direct coevolutionary couplings reflect biophysical residue interactions in proteins. Semantic Scholar is a free, AI-powered research tool for scientific literature, based at the Allen Institute for AI. The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. INPUT DATA Data are given as a multiple sequence alignment Direct-coupling analysis of residue coevolution captures native contacts across many protein families 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. 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. Direct coupling analysis for protein contact prediction. 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. 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. Faruck Morcos Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0374, USA. 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. The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. You are currently offline. Crucial to this inference is the ability to disentangle direct and indirect correlations, as accomplished by the recently introduced direct-coupling analysis (DCA). Crucial to this inference is the ability to disentangle direct and indirect correlations, as accomplished by the recently introduced direct-coupling analysis (DCA). 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. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Astrophysical Observatory. Agreement NNX16AC86A, Proceedings of the National Academy of Science, Is ADS down? 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. How Pairwise Coevolutionary Models Capture the Collective Residue Variability 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 … (or is it just me...), Smithsonian Privacy The ADS is operated by the Smithsonian Astrophysical Observatory under NASA Cooperative 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. Inference of direct residue contacts in two-component signaling. Quantitative Biology - Quantitative Methods; Condensed Matter - Statistical Mechanics. Use, Smithsonian Onuchic, T. Hwa, and M. Weigt I. 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. Crucial to this inference is the ability to disentangle direct and indirect correlations, as accomplished by the recently introduced direct-coupling analysis (DCA….
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