A Database of Protein Topographic Surfaces from Computational Geometry

University Of Illinois At Chicago, Chicago IL

Investigators

Abstract

The objectives of this proposal are to develop informatics tools to characterize the voids, pockets and tunnels that characterize protein surfaces and to construct a database of protein surface maps. The topographic of the protein helps to define the binding regions essential for the protein's functions. Understanding protein surface properties is basic to understanding interactions with other proteins as well as other small ligands. Such information may provide a way to identify active sites. The tools generate not only the maps of the surface, with area and volume measurement, but also measure the accessibility of binding pockets from the outside of the molecule and the texture of the surfaces. The description can be computed also at different levels of resolution. This research has the potential for linking structure with function by providing information about the possible sites of interaction between and among molecules. In addition, the work will provide an educational resource for understanding protein geometry.