Quasi-Physical Algorithm of an Off-Lattice Model for Protein Folding Problem

Protein folding problem is one of the most prominentproblems of bioinformatics. In this paper, we study a three-dimensionaloff-lattice protein AB model with two species of monomers, hydrophobicand hydrophilic, and present a heuristic quasi-physical algorithm.By elaborately simulating the movement of the smooth elasticballs in the physical world, the algorithm finds low-energyconfigurations for a given monomer chain. A subsequent ``off-trap''strategy is proposed to trigger a jump for a stuck situation in orderto get out of local minima. The methods have been tested in theoff-lattice AB model. The computational results show promisingperformance. For all sequences with 13 to 55 monomers, the algorithmfinds states with lower energy than previously proposed putative groundstates. Furthermore, for the sequences with 21, 34 and 55 monomers,new putative ground states are found, which are different from thosegiven in present literature.