Contact prediction is hardest for the most informative contacts, but improves with the incorporation of contact potentials.

ABSTRACT: Co-evolution between pairs of residues in a multiple sequence alignment (MSA) of homologous proteins has long been proposed as an indicator of structural contacts. Recently, several methods, such as direct-coupling analysis (DCA) and MetaPSICOV, have been shown to achieve impressive rates of contact prediction by taking advantage of considerable sequence data. In this paper, we show that prediction success rates are highly sensitive to the structural definition of a contact, with more permissive definitions (i.e., those classifying more pairs as true contacts) naturally leading to higher positive predictive rates, but at the expense of the amount of structural information contributed by each contact. Thus, the remaining limitations of contact prediction algorithms are most noticeable in co

SUBMITTER: Holland J 

PROVIDER: S-EPMC6023208 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature