Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction.

ABSTRACT: Compensatory mutations between protein residues in physical contact can manifest themselves as statistical couplings between the corresponding columns in a multiple sequence alignment (MSA) of the protein family. Conversely, large coupling coefficients predict residue contacts. Methods for de-novo protein structure prediction based on this approach are becoming increasingly reliable. Their main limitation is the strong systematic and statistical noise in the estimation of coupling coefficients, which has so far limited their application to very large protein families. While most research has focused on improving predictions by adding external information, little progress has been made to improve the statistical procedure at the core, because our lack of understanding of the sources of nois

SUBMITTER: Vorberg S 

PROVIDER: S-EPMC6237422 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature