Protein Docking using Elevation
by
Pankaj K. Agarwal
Duke University

Given a smoothly embedded 2-manifold in 3-space, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold, which is invariant under rigid motions. Elevation is used to define features such as lines of discontinuous or continuous but non-smooth elevation on surfaces. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions on molecular surfaces. By aligning these features on protein surfaces we present an efficient algorithm to generate a reasonably small but reliable set of coarse protein docking configurations, and then use an iterative algorithm to locally improve the docking configuration. A protein is considered as a rigid body in our approach, and the output produced can serve as input data for other local improvement methods that allow protein flexibility. We demonstrate the performance of our algorithm by testing our algorithm on a diverse set of protein complexes from the Protein Data Bank.

Date received: February 6, 2005