Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns.

ABSTRACT: Inferring protein functions from structures is a challenging task, as a large number of orphan protein structures from structural genomics project are now solved without their biochemical functions characterized. For proteins binding to similar substrates or ligands and carrying out similar functions, their binding surfaces are under similar physicochemical constraints, and hence the sets of allowed and forbidden residue substitutions are similar. However, it is difficult to isolate such selection pressure due to protein function from selection pressure due to protein folding, and evolutionary relationship reflected by global sequence and structure similarities between proteins is often unreliable for inferring protein function. We have developed a method, called pevoSOAR (pocket-based evo

SUBMITTER: Tseng YY 

PROVIDER: S-EPMC2670802 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature