Berlin 2008 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 25: Protein Structure and Folding

BP 25.2: Vortrag

Donnerstag, 28. Februar 2008, 14:45–15:00, PC 203

Algorithm for selection of fast folding proteins — •Dmitry Gridnev and Martin Garcia — Kassel University, Heinrich-Plett-Str. 40, Germany

We discuss the following problem: from a large number of given amino acid chains select potentially good folders. In the framework of the lattice model of proteins we propose an algorithm, which uses the Monte Carlo dynamics and tests the rate of convergence of an amino acid chain in the configuration space. To test this algorithm we have hidden one known good folder among one thousand of other chains with a random amino acid decomposition. Our results show that the designed good folding sequence comes on top in the list of folders from good to bad. We also discuss how this method could be generalized to more sophisticated atomistic models.