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Published on: July 25, 2013
A quasi-physical algorithm for the structure optimization in an off-lattice protein model
1School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China. ljf720622@163.com
Abstract:
In this paper, we study an off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. First, by elaborately simulating the movement of the smooth solids in the physical world, we find low-energy conformations for a given monomer chain. A subsequent off-trap strategy is then proposed to trigger a jump for a stuck situation in order to get out of the local minima. The algorithm has been tested in the three-dimensional AB model for all sequences with lengths of 13-55 monomers. In several cases, we renew the putative ground state energy values. The numerical results show that the proposed methods are very promising for finding the ground states of proteins.
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