Talk presented by Carsten Peterson

Parallel Session: Spin Models II

Thursday July 1st, 17.00 - 17.20, Room B

Folding and Design in Coarse-Grained Protein Models

Abstract: Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. In these models the amino acid residues, which represent the degrees of freedom, are binary; hydrophobic and hydrophilic respectively. The sequence dependence of thermodynamical properties of good folders are investigated and evidence for non-randomness of the binary sequence is established for the latter. Similar patterns for non-randomness are found for real proteins. Dynamical parameter MC methods, such as the tempering and multisequence algorithms, are essential in order to obtain these results. Design, the inverse problem to folding, where a sequence is optimized to have a fixed structure as a stable ground state, have also been studied. A new MC method for this problem is presented, where conditional probabilities are maximized rather than minimizing energy functions. By construction, this method ensures that the designed sequences represent good folders thermodynamically. Tests of this sequence design procedure exhibits high efficiency.

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