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International Journal of Pharmacology and Pharmaceutical Technology

Abstract

Current methods for protein analysis are based on either sequence similarity or comparison of overall tertiary structure. These conserved primary sequences or 3-dimensional structures may imply similar functional characteristics. However, substrate or ligand binding sites usually reside on or near protein surface, so, similarly shaped surface regions could imply similar functions. Our current work includes development of an algorithm that would allow surface matching over specific regions on related proteins with an output equal to the match percentage between two proteins. Initial results indicate that we can successfully match a family of related active sites, and find their similarly shaped surface regions. This method of surface analysis could be extended to help us understand functional surface relationship between the proteins within which there is no relationship in sequence or overall structure.

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