ABSTRACT
Although the 3D structures of more than 50,000 proteins have been determined and recorded in the Protein Data Bank (PDB) to date (Berman et al. 2000), accurate structural modeling of unknown proteins remains one of the most challenging problems in molecular biology. Modeling the protein structure, which involves determining the optimum side-chain conformations as well as backbone geometry, is important to understand molecular function because the activity of a protein often depends critically on its structure. For example, to understand enzymatic catalysis at a molecular level, one must rst understand the structural aspects of the active site, including the elaborate tertiary arrangement of side chain and backbone atoms.
