A challenge in structural genomics is prediction of the function of uncharacterized proteins. When proteins cannot be related to other proteins of known activity, identification of function based on sequence or structural homology is impossible and in such cases it would be useful to identify and assess structurally conserved binding sites in connection with the protein's function. Experimental identification of protein function is the most reliable way to characterize proteins of unknown activity but it is difficult to prioritize functional experiments amongst the many possible functions a protein could perform. To guide experimental scientists, a number of computer approaches have been developed for prediction of protein function. In this paper, we investigate a new strategy to predict protein function employing ProBiS enhanced by molecular dynamics simulation, to find structurally evolutionarily conserved binding sites on a protein of unknown function. The strategy uses ProBiS to find the active sites in the protein followed by searches in the PDB for active sites with similar physicochemical and geometric properties and molecular dynamics analysis of the possible enzyme-ligand complexes. The functional characterization in this way of a previously uncharacterized protein will be described.

Structure-based function prediction for proteins of unknown function employing ProBiS enhanced by molecular dynamics

246th National Meeting (2013)

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