Computational protein folding: From lattice to all-atom

Understanding the mechanism of protein folding is often referred to as the second half of genetics. Computational approaches have been instrumental in the efforts. Simplified models have been applied to understand the physica l principles governing the folding processes and will continue to play impo rtant roles in the endeavor. Encouraging results have been obtained from al l-atom molecular dynamics simulations of protein folding. A recent microsec ond-length molecular dynamics simulation on a small protein, villin headpie ce subdomain, with an explicit atomic-level representation of both protein and solvent, has marked the beginning of direct and realistic simulations o f the folding processes. With growing computer power and increasingly accur ate representations together with the advancement of experimental methods, such approaches will help us to achieve a detailed understanding of protein folding mechanisms.