An Experimental Shape Matching Approach for Protein Docking

Abstract

Proteins play a vital role in biological processes, with their function being largely determined by their structure. It is important to know what a protein binds, where it binds, how it binds, and what is its final conformation. Several methodologies have been applied to solve this complex protein-protein docking problem, but the number of degrees of freedom renders this a very slow and computationally heavy challenge. To handle this problem, we propose a multi-level space partition approach to describe the three-dimensional shape of the protein. By combining two proteins in the same data structure we are able to easily detect the shape-complementary regions. Moreover, by directly integrating bio-energetic information, we can drive the algorithm by both parameters and provide a fast and efficient way to overcome some of the limitations of previous approaches.