CovET: A covariation-evolutionary trace method that identifies protein structure–function modules

Rheostats, toggles, and neutrals, Oh my! A new framework for understanding how amino acid changes modulate protein function

“…Second, within an MSA, several types of “nonconservation” can occur: Changes at some pairs (or larger clusters) of positions are correlated, suggesting that they co-evolve ( e.g. , ( 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 )). At other positions, amino acid changes correlate with the branch points of the MSA’s phylogenetic tree ( e.g.…”