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| Wolfgang Wenzel, University of Karslruhe |
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| Wolfgang Wenzel is presently the group-leader for computational bionanophysics at the Institute for Nanotechnology at the Research Center Karlsruhe, one of Germany's national laboratories. He is also a member of the faculty of the department of physics at Dortmund University. He obtained his Ph. D. in solid state physics in 1989 at Ohio State University, where he stayed for a postdoctoral appointment with K.G. Wilson in quantum chemistry. He then joined the physics department of Dortmund University, where he obtained his habilitation in 1997. In 2001 he joined the present group at the research center Karlsruhe. His research interests include molecular electronics, protein folding and in-silico drug design (www.fzk.de/biostruct).
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All-atom protein folding with stochastic optimization methods
A. Schug , A. Verma and W. Wenzel, Forschungszentrum Karlsruhe, Institut für Nanotechnologie, Karlsruhe, Germany
The prediction of protein tertiary structure, in particular based on sequence information alone, remains one of the outstanding problems in biophysical chemistry. We have recently developed an all-atom free energy forcefield (PFF01) which implements a minimal thermodynamic model based on physical interactions and an implicit solvent model. We could demonstrate that PFF01 stabilizes the native conformation of several helical proteins as the global optimum of its free energy surface. In addition we were able to reproducibly fold several helical proteins, ranging 20-60 amino acids in size from random starting conditions. We used several stochastic optimization methods: the stochastic tunneling method, an adapted version of parallel tempering, basin hopping techniques and distributed evolutionary optimization strategies. We will discuss advantages and limitations with respect to further improvements of this approach to in-silico all-atom protein structure prediction.
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