Evolutionary approach to predicting the binding site residues of a protein from its primary sequence.

ABSTRACT: Protein binding site residues, especially catalytic residues, play a central role in protein function. Because more than 99% of the ∼ 12 million protein sequences in the nonredundant protein database have no structural information, it is desirable to develop methods to predict the binding site residues of a protein from its primary sequence. This task is highly challenging, because the binding site residues constitute only a small portion of a protein. However, the binding site residues of a protein are clustered in its functional pocket(s), and their spatial patterns tend to be conserved in evolution. To take advantage of these evolutionary and structural principles, we constructed a database of ∼ 50,000 templates (called the pocket-containing segment database), each of which includes not

SUBMITTER: Tseng YY 

PROVIDER: S-EPMC3069214 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature