International Journal of Information Engineering and Electronic Business (IJIEEB)
IJIEEB Vol. 3, No. 1, 8 Feb. 2011
Cover page and Table of Contents: PDF (size: 627KB)
An Improved Particle Swarm Optimization for Protein Folding Prediction
Full Text (PDF, 627KB), PP.1-8
Views: 0 Downloads: 0
Author(s)
Xin Chen
1,*
Mingwei Lv
1
Lihui Zhao
1
Xudong Zhang
1
Index Terms
Protein Folding Prediction, Particle Swarm Optimizer, Levy Flight, 3D AB off-lattice model
Abstract
In this paper, we combine particle swarm optimization (PSO) and levy flight to solve the problem of protein folding prediction, which is based on 3D AB off-lattice model. PSO has slow convergence speed and low precision in its late period, so we introduce levy flight into it to improve the precision and enhance the capability of jumping out of the local optima through particle mutation mechanism. Experiments show that the proposed method outperforms other algorithms on the accuracy of calculating the protein sequence energy value, which is turned to be an effective way to analyze protein structure.
Cite This Paper
Xin Chen, Mingwei Lv, Lihui Zhao, Xudong Zhang, "An Improved Particle Swarm Optimization for Protein Folding Prediction", International Journal of Information Engineering and Electronic Business(IJIEEB), vol.3, no.1, pp.1-8, 2011. DOI:10.5815/ijieeb.2011.01.01
Reference
[1]G.A.Petsko. Structure and mechanism in protein science:A guide to enzyme catalysis and protein folding[J]. Nature, 2003,401(6749): 115-116.
[2]Anfinsen C B. Principles that Govern the Folding of Protein Chains[J]. Science,1973,181(4096): 223-227.
[3]T.Lazaridis and M.Karplus.”New view” of protein folding reconciled with the old through multiple unfolding simulations [J].Science.2004,278(5):1928-1931.
[4]K.A.Dill. Dominant forces in protein folding [J].Biochemistry, 1990,29:7133-7155.
[5]F.H.Stillinger, H.Gordon, C.L.Hirshfeld. Toy model for protein folding [J]. Physical Review E, 1993,48:1469-1477.
[6]F.H.Stillinger. Collective aspects of protein folding illustrated by a toy model [J].Physical Review E, 1992,52(32):2872-2877.
[7]D. Chu, N. Till and A. Zomaya. Parallel Ant Colony Optimization for 3D Protein Structure Prediction using the HP off Lattice Model [C].Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium.2006.
[8]Xiaolong Zhang, Wen Cheng. An Improved Tabu Search Algorithm for 3D protein Folding Problem[J]. Computer Science, 2008,5351:1104-1109. (in Chinese)
[9]Xiaolong Zhang, Xiaoli Lin,Chengpeng Wan, Tingting Li. Genetic-Annealing Alogorithm for 3D Off-lattice Protein Folding Model[J]. Emerging Technologies in Knowledge Discovery and Data Mining, 2009,4819: 186-193.
[10]K. A. Dill. Theory for the Folding and Stability of Globular Proteins [J]. Biochemistry. 1985, 24(6): 1501-1509.
[11]Kennedy J,Eberhart R. Particle swarm optimization [J] IEEE International Conference on Neural Networks Conference Proceedings. Perth, Aust, 1995 :1942-1948.
[12]K.F.Lau,K.A.Dill.A Lattice Statistical Mechanics Model of the Conformation and Sequence Space of Proteins [J].Macromolecules.1992,22(10):3968-3997.
[13]K.A.Dill,H.S.Chan. From Levinthal to pathways to funnels [J]. Nature Structural & Molecular Biology.1997,4(1):10-19.
[14]E. Weeks, T. Solomon, J. Urbach, and H. Swinney, "Observation of anomalous diffusion and L¨¦vy flights," [J] Le¦vy Flights and Related Topics in Physics, pp. 51-71, 1995.
[15]R. Weron, "Levy-stable distributions revisited: tail index> 2 does not exclude the Levy-stable regime," [J] Arxiv preprint cond-mat/0103256, 2001.
[16]M. Gutowski, "Levy flights as an underlying mechanism for global optimization algorithms," [J] Arxiv preprint math-ph/0106003, 2001.
[17]A. Kubala-Kuku, D. Bana, J. Braziewicz, U. Majewska, and M. Pajek, "Concentration distribution of trace elements: from normal distribution to Lévy flights* 1," [J] Spectrochimica Acta Part B: Atomic Spectroscopy, vol. 58, pp. 717-724, 2003.
[18]G. Viswanathan, V. Afanasyev, S. Buldyrev, E. Murphy, P. Prince, and H. Stanley, "Levy flight search patterns of wandering albatrosses,"[J] Nature, vol. 381, pp. 413-415, 1996.
[19]N. Humphries, N. Queiroz, J. Dyer, N. Pade, M. Musyl, K. Schaefer, D. Fuller, J. Brunnschweiler, T. Doyle, and J. Houghton, "Environmental context explains Levy and Brownian movement patterns of marine predators," Nature, 2010.