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CLC number: TP3; Q67
On-line Access: 2024-08-27
Received: 2023-10-17
Revision Accepted: 2024-05-08
Crosschecked: 0000-00-00
Cited: 14
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Heuristic algorithm for off-lattice protein folding problem
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Chen Mao, Huang Wen-qi. Heuristic algorithm for off-lattice protein folding problem[J]. Journal of Zhejiang University Science B, 2006, 7(1): 7-12.
@article{title="Heuristic algorithm for off-lattice protein folding problem",
author="Chen Mao, Huang Wen-qi",
journal="Journal of Zhejiang University Science B",
volume="7",
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pages="7-12",
year="2006",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2006.B0007"
}
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%A Chen Mao
%A Huang Wen-qi
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%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2006.B0007
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T1 - Heuristic algorithm for off-lattice protein folding problem
A1 - Chen Mao
A1 - Huang Wen-qi
J0 - Journal of Zhejiang University Science B
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EP - 12
%@ 1673-1581
Y1 - 2006
PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.2006.B0007
Abstract: Enlightened by the law of interactions among objects in the physical world, we propose a heuristic algorithm for solving the three-dimensional (3D) off-lattice protein folding problem. Based on a physical model, the problem is converted from a nonlinear constraint-satisfied problem to an unconstrained optimization problem which can be solved by the well-known gradient method. To improve the efficiency of our algorithm, a strategy was introduced to generate initial configuration. Computational results showed that this algorithm could find states with lower energy than previously proposed ground states obtained by nPERM algorithm for all chains with length ranging from 13 to 55.
[1] Anfinsen, C., 1973. Principles that govern the folding of protein chains. Science, 181:223-230.
[2] Bachmann, M., Arkın, H., Janke, W., 2005. Multicanonical study of coarse-grained off-lattice models for folding heteropolymers. Phys. Rev. E, 71:031906.
[3] Crescenzi, P., Goldman, D., Papadimitriou, C., Piccolboni, A., Yannakakis, M., 1998. On the complexity of protein folding. Journal of Computational Biology, 5(3):409-422.
[4] Dill, K.A., 1985. Theory for the folding and stability of globular proteins. Biochemistry, 24:1501-1509.
[5] Hsu, H.P., Mehra, V., Grassberger, P., 2003. Structure optimization in an off-lattice protein model. Phys. Rev. E, 68:037703.
[6] Irback, A., Peterson, C., Potthast, F., 1997. Identification of amino acid sequences with good folding properties in an off-lattice model. Phys. Rev. E, 55:860-867.
[7] Kim, S.Y., Lee, S.B., Lee, J., 2005. Structure optimization by conformational space annealing in an off-lattice protein model. Phys. Rev. E, 72:011916.
[8] Lau, K.F., Dill, K.A., 1989. A lattice statistical mechanics model of the conformational and sequence space of proteins. Macromolecules, 22:3986-3997.
[9] Stillinger, F.H., 1995. Collective aspects of protein folding illustrated by a toy model. Phys. Rev., 52:2872-2877.
[10] Torcini, A., Livi, R., Politi, A., 2001. A dynamical approach to protein folding. J. Biol. Phys., 27:181-186.
[11] Wang, H.Q., Huang, W.Q., Zhang, Q., Xu, D.M., 2002. An improved algorithm for the packing of unequal circles within a larger containing circle. European Journal of Operational Research, 141:440-453.
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