ITR: Computational Geometry for Structural Biology and Bioinformatics

Duke University, Durham NC

Investigators

Abstract

Life at its most detailed level depends on the geometric shape of molecules. Nevertheless, geometric methods are relatively uncommon in computational biology, primarily because of difficult and unsolved issues in applying geometric computing to biology. This project will address these causes by investigating geometric representations and developing novel geometric methods. It will incorporate these into software that helps structural biologists with their work and integrates with their current tools. The key research issues include: 1)representation and classification of geometric shape; 2)synthesis of geometric, physical, and statistical information; 3)computation and representation of motion; 4)organization of shapes for rapid searches; and 5) hierarchies for everything. This research is expected to shed light on some of the most important unsolved biological puzzles: prediction of protein structure, simulation of protein folding, and analysis of ligand to protein docking. These processes link form to function. Understanding them will pave the way to a post-genomic era in biological research, in which the wealth of DNA sequence information is complemented by corresponding knowledge of geometric shape. Together, sequence and shape will provide a description of the biological function so critical for all life.