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Journal articles
Direct coevolutionary couplings reflect biophysical residue interactions in proteins
Abstract : Coevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21 x 21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices. Published by AIP Publishing.
https://hal.archives-ouvertes.fr/hal-01528504
Contributor : Administrateur Hal-Upmc <>
Submitted on : Monday, May 29, 2017 - 11:25:03 AM
Last modification on : Thursday, December 10, 2020 - 12:36:35 PM
Contributor : Administrateur Hal-Upmc <>
Submitted on : Monday, May 29, 2017 - 11:25:03 AM
Last modification on : Thursday, December 10, 2020 - 12:36:35 PM
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