Accurate prediction of substitution rates at protein sites with a mutation-selection model.

ABSTRACT: The pattern of substitutions at sites in proteins provides invaluable information about their biophysical and functional importance and what selection pressures are acting at individual sites. Amino acid site rates are typically estimated using phenomenological models where sequence variability is described by rate factors that scale the overall substitution rate in a protein to sites. In this study, we demonstrate that site rates can be calculated accurately from amino acid sequences from a multiple sequence alignment using a mutation-selection model in combination with a simple nucleotide substitution model. The method performs better than the standard phylogenetic approach on sequences generated by structure-based evolutionary dynamics simulations, robustly estimates rates for shallow m

SUBMITTER: Andre I 

PROVIDER: S-EPMC12491638 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature