Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups as interaction sites is p resented. The model is designed to work in continuous space; hence efficien t global-optimization methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the orig inal rugged energy hypersurface to obtain a smoothed surface. The method ha s been applied successfully to predict the structures of simple motifs. suc h as the three-helix bundle structure of the 10-58 fragment of staphylococc al protein A in de novo folding simulations and more complicated motifs in inverse-folding simulations.