Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures.

ABSTRACT: Substitutions of individual amino acids in proteins may be under very different evolutionary restraints depending on their structural and functional roles. The Environment Specific Substitution Table (ESST) describes the pattern of substitutions in terms of amino acid location within elements of secondary structure, solvent accessibility, and the existence of hydrogen bonds between side chains and neighbouring amino acid residues. Clearly amino acids that have very different local environments in their functional state compared to those in the protein analysed will give rise to inconsistencies in the calculation of amino acid substitution tables. Here, we describe how the calculation of ESSTs can be improved by discarding the functional residues from the calculation of substitution tables.

SUBMITTER: Gong S 

PROVIDER: S-EPMC2527532 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature