Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families.

ABSTRACT: The increasing volume of genomic data opens new possibilities for analysis of protein function. We introduce a method for automated selection of residues that determine the functional specificity of proteins with a common general function (the specificity-determining positions [SDP] prediction method). Such residues are assumed to be conserved within groups of orthologs (that may be assumed to have the same specificity) and to vary between paralogs. Thus, considering a multiple sequence alignment of a protein family divided into orthologous groups, one can select positions where the distribution of amino acids correlates with this division. Unlike previously published techniques, the introduced method directly takes into account nonuniformity of amino acid substitution frequencies. In addi

SUBMITTER: Kalinina OV 

PROVIDER: S-EPMC2286703 | biostudies-literature | 2004 Feb

REPOSITORIES: biostudies-literature