Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.

ABSTRACT: A critical question in biology is the identification of functionally important amino acid sites in proteins. Because functionally important sites are under stronger purifying selection, site-specific substitution rates tend to be lower than usual at these sites. A large number of phylogenetic models have been developed to estimate site-specific substitution rates in proteins and the extraordinarily low substitution rates have been used as evidence of function. Most of the existing tools, e.g. Rate4Site, assume that site-specific substitution rates are independent across sites. However, site-specific substitution rates may be strongly correlated in the protein tertiary structure, since functionally important sites tend to be clustered together to form functional patches. We have developed a

SUBMITTER: Huang YF 

PROVIDER: S-EPMC3894161 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature