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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

http://doi.org/10.1631/jzus.2006.B0007


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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journal="Journal of Zhejiang University Science B",
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publisher="Zhejiang University Press & Springer",
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%A Huang Wen-qi
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TY - JOUR
T1 - Heuristic algorithm for off-lattice protein folding problem
A1 - Chen Mao
A1 - Huang Wen-qi
J0 - Journal of Zhejiang University Science B
VL - 7
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EP - 12
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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.

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

Reference

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[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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