Application of Systematic Conformational Search to Protein Modeling

Abstract

Systematic conformational search is a powerful tool in the modeling of proteins and peptides. As a deterministic method for sampling comformational space, it provides an efficient mechanism for finding global energy minima. The program CONGEN has been developed to use conformational search in conjunction with other modeling methods. The search operators in CONGEN can be combined in arbitrary ways, and therefore, they can applied to a wide variety of problems. Typical applications include homology modeling, construction of protein coordinates from C_α positions, sidechain placement, peptide structure modeling, derivation of three-dimensional structure from NMR constraints, etc. In this paper, a detailed description will be provided of its conformational search capabilities and its previous applications to protein modeling.