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  • To fill this gap, this paper describes VASP-E (Volumetric Analysis of Surface Properties with Electrostatics), a novel volumetric comparison tool based on the electrostatic comparison of protein-ligand and protein-protein binding sites. These results suggest that VASP-E should prove a useful tool for the characterization of specific binding and the engineering of binding preferences in proteins. Our approach identifies regions like these by representing electrostatic isopotentials with volumetric solids generated by the new program VASP-E (Volumetric Analysis of Surface Properties with Electrostatics). Because VASP-E is designed to identify electrostatic influences on specificity, we validate it using families of proteins for which the mechanisms that achieve specificity are well understood and fundamentally electrostatic. VASP-E was developed in ansi C/C++ using gcc (the Gnu Compiler Collection) version 4.4.7, on 64 bit linux-based computing platforms.
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