3D Protein Structure Prediction with Local Adjust Tabu Search Algorithm

The protein folding structure prediction is computationally challenging and has been shown to be NP-hard when the 3D off-lattice AB model is employed. In this paper, the local adjustment tabu search (LATS) algorithm has been used to search the ground state of 3D AB off-lattice model for protein folding structure. A kind of optimization about the neighborhood scale and the annealing mechanism has been presented, where a local adjustment strategy has also been used to enhance the searching ability for the global minimum within theAB off-lattice model. Experimental results demonstrate that the proposed algorithm has better performance in global optimization and can predict 3D protein structure more effectively.

[1]  Kim Allan Andersen,et al.  A Tabu Search Approach to Clustering , 2009 .

[2]  John Lygeros,et al.  Simulated Annealing: Rigorous finite-time guarantees for optimization on continuous domains , 2007, NIPS.

[3]  William E. Hart,et al.  Protein Structure Prediction with Lattice Models , 2006 .

[4]  Heitor Silvério Lopes.  Evolutionary Algorithms for the Protein Folding Problem: A Review and Current Trends , 2008, Computational Intelligence in Biomedicine and Bioinformatics.

[5]  Yi Wang,et al.  Multiple Sequence Alignment Using Tabu Search , 2004, APBC.

[6]  Christopher J. Gatti,et al.  Optimization of Muscle Wrapping Objects Using Simulated Annealing , 2009, Annals of Biomedical Engineering.

[7]  Faming Liang,et al.  Annealing contour Monte Carlo algorithm for structure optimization in an off-lattice protein model. , 2004, The Journal of chemical physics.

[8]  Jooyoung Lee,et al.  Structure optimization by conformational space annealing in an off-lattice protein model. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[9]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[10]  Frank Potthast,et al.  Local interactions and protein folding: A three-dimensional off-lattice approach , 1997 .

[11]  Xiaolong Zhang,et al.  Genetic-Annealing Algorithm for 3D Off-lattice Protein Folding Model , 2007, PAKDD Workshops.

[12]  K. Dill.  Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[13]  Wolfhard Janke,et al.  Multicanonical study of coarse-grained off-lattice models for folding heteropolymers. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[14]  Xiao-Long Zhang,et al.  Effective 3D protein structure prediction with local adjustment genetic-annealing algorithm , 2010, Interdisciplinary Sciences: Computational Life Sciences.

[15]  Hsiao-Ping Hsu,et al.  Structure optimization in an off-lattice protein model. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[16]  Head-Gordon,et al.  Collective aspects of protein folding illustrated by a toy model. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[17]  Hongbing Zhu,et al.  Structure Optimization by an Improved Tabu Search in the AB Off-Lattice Protein Model , 2008, 2008 First International Conference on Intelligent Networks and Intelligent Systems.

[18]  Hongbing Zhu,et al.  Protein Structure Prediction with EPSO in Toy Model , 2009, 2009 Second International Conference on Intelligent Networks and Intelligent Systems.