ABSTRACT
We recently developed an all-atom free energy forcefield (PFF01) for protein structure prediction with stochastic optimization methods. Here we review recent folding studies, which permitted the reproducible all-atom folding of the (i) 20 amino-acid trpcage protein, (ii) the 36 amino acid villin headpiece, (iii) the 40-amino acid three-helix HIV accessory protein and (iv) the sixty amino acid bacterial ribosomal protein L20 with a variety of stochastic optimization methods. We could also demonstrate that PFF01 stabilized the native folds of various other proteins ranging from 40-60 amino acids at the all atom level. We compare the efficiency of different stochastic optimization methods for protein folding and give a brief outlook on the perspective of our thermodynamic approach.
