All atom protein folding: A progress report

Abstract

De novo protein structure prediction remains an important challenge to biophysical chemistry and computer science. We could demonstrate that a recently developed an all-atom free energy forcefield (PFF01) stabilizes the native conformation of several proteins as the global optimum of the free energy surface. Here we review recent folding studies, which permitted the reproducible all-atom folding of the 20 amino-acid trp-cage protein, the 40-amino acid three-helix HIV accessory protein and the sixty amino acid bacterial ribosomal protein L20 with a variety of stochastic optimization methods. These results demonstrate that all-atom protein folding can be achieved with present day computational resources for proteins of moderate size.