2014 Volume 54 Issue 2 Pages 091-095
Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function put structural and functional constraints in varying degrees on each residue site. Coevolution between closely-located sites caused by such selective constraints is recorded in amino acid orders of homologous sequences and also in the evolutionary trace of amino acid substitutions. A challenge for predicting residue contacts through coevolving site pairs is to extract direct dependences between sites by removing phylogenetic correlations and indirect dependences through other residues within a protein or even through other molecules. Recent attempts, particularly by detecting co-substitutions, are reviewed.