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CLC number: TP3; Q67

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Received: 2005-08-10

Revision Accepted: 2005-11-28

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Journal of Zhejiang University SCIENCE B 2006 Vol.7 No.1 P.7~12


Heuristic algorithm for off-lattice protein folding problem

Author(s):  Chen Mao, Huang Wen-qi

Affiliation(s):  School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China

Corresponding email(s):   mchen_1@163.com

Key Words:  Protein folding, AB off-lattice model, Gradient method

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.

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publisher="Zhejiang University Press & Springer",

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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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PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.2006.B0007

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.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[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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