Annealing contour Monte Carlo algorithm for structure optimization in an off-lattice protein model.

Abstract

We present a space annealing version for a contour Monte Carlo algorithm and show that it can be applied successfully to finding the ground states for an off-lattice protein model. The comparison shows that the algorithm has made a significant improvement over the pruned-enriched-Rosenbluth method and the Metropolis Monte Carlo method in finding the ground states for AB models. For all sequences, the algorithm has renewed the putative ground energy values in the two-dimensional AB model and set the putative ground energy values in the three-dimensional AB model.