A quasi-physical algorithm for the structure optimization in an off-lattice protein model |
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Authors: | Liu Jing-Fa Huang Wen-Qi |
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Affiliation: | School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China. ljf720622@163.com |
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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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Keywords: | protein folding off-lattice model quasi-physical algorithm off-trap strategy |
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