As of April 2012, there are 11009 protein structures deposited by structural genomics (SG) centers in the PDB with 'putative' or 'unknown' functional annotations.  We describe a method utilizing two computational functional site predictors, THEMATICS and POOL, which identify catalytic and binding residues, to help assign function to SG proteins using Structurally Aligned Local Sites of Activity (SALSA). To implement SALSA, we first identify a set of structurally similar proteins with functionally diverse subsets.  A 3D structure match at the predicted, local functional site then serves as a more reliable predictor of biochemical function than an overall structure match.  The method is validated with sets of well-characterized proteins from the ribulose phosphate-binding barrel (RPBB) superfamily.  Ten SG proteins with putative functions were found in the PDB and correctly annotated. The SALSA method demonstrates accuracy in identification of subclasses and streamlines the assignment of function for the SG proteins.

Functional assignment of structural genomics proteins in the ribulose-phosphate binding barrel superfamily

244th National Meeting (2012)

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