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Published in:
2006 | OriginalPaper | Chapter
STOCHASTICOPTIMIZATION METHODS FOR PROTEIN FOLDING
Authors : ALEXANDER SCHUG, THOMAS HERGES, ABHINAV VERMA, WOLFGANG WENZEL
Published in: Recent Advances in the Theory of Chemical and Physical Systems
Publisher: Springer Netherlands
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We recently developed an all-atom free energy force field (PFF01) for protein structure prediction with stochastic optimization methods. We demonstrated that PFF01 correctly predicts 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.