Anders Irbäck
Dynamical-Parameter Algorithms for Protein Folding
Workshop on Monte Carlo Approach to Biopolymers and Protein Folding, eds. P. Grassberger, G.T. Barkema and W. Nadler, pp. 98-109 (World Scientific, Singapore, 1998)

Abstract:
Two different dynamical-parameter algortihms are discussed, simulated tempering and the multisequence method. Using simulated tempering, the folding properties of 300 random sequences in a simple off-lattice model with only two amino-acid types, hydrophobic and hydrophilic, are investigated. A careful statistical analysis shows that the hydrophobic monomers are anticorrelated along the chains for good folding sequences. The multisequence method is the basis for a novel procedure for maximizing the stability of a given target structure. Tests of this sequence design procedure on the HP lattice model show that it can be extremely efficient.

LU TP 98-06