The analysis of protein surfaces to detect small ligand or protein binding sites has important applications in structure based drug discovery and functional assignment. We propose to develop an integrated protein surface analysis and graphics tool that will allow users to apply several binding site prediction methods and visualize the results. It is expected that the multiple detection methods will yield a more accurate prediction result. 2 novel protein surface analysis algorithms will also be implemented and included in the software suite. First, we will optimize a previously developed protein-protein interface prediction method to detect small molecule binding sites. The other algorithm is a surface structural motif detection and visualization method. The output of the algorithm is a graph, so we will evaluate graph comparison measures with the goal of developing a fast database search method. The surface annotation suite will be marketed as a separate module for the ICM molecular modelling package and oriented towards use by biologists and biochemists. ? ? ?
| Totrov, Maxim (2011) Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites. BMC Bioinformatics 12 Suppl 1:S35 |
