Structural constraints on the covariance matrix derived from multiple aligned protein sequences.

ABSTRACT: Residue contact predictions were calculated based on the mutual information observed between pairs of positions in large multiple protein sequence alignments. Where previously only the statistical properties of these data have been considered important, we introduce new measures to impose constraints that make the contact map more consistent with a three dimensional structure. These included global (bulk) properties and local secondary structure properties. The latter allowed the contact constraints to be employed at the level of filtering pairs of secondary structure contacts which led to a more efficient (lower-level) implementation in the PLATO structure prediction server. Where previously the measure of success with this method had been whether the correct fold was predicted in the top

SUBMITTER: Taylor WR 

PROVIDER: S-EPMC3237328 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature