On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins.

ABSTRACT: Coevolution-based contact prediction, either directly by coevolutionary couplings resulting from global statistical sequence models or using structural supervision and deep learning, has found widespread application in protein-structure prediction from sequence. However, one of the basic assumptions in global statistical modeling is that sequences form an at least approximately independent sample of an unknown probability distribution, which is to be learned from data. In the case of protein families, this assumption is obviously violated by phylogenetic relations between protein sequences. It has turned out to be notoriously difficult to take phylogenetic correlations into account in coevolutionary model learning. Here, we propose a complementary approach: we develop strategies to randomi

SUBMITTER: Rodriguez Horta E 

PROVIDER: S-EPMC8177639 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature