Flexible ligand docking using differential evolution

2003 Congress on Evolutionary Computation, CEC 2003 - Proceedings

Volumn 4, Issue , 2003, Pages 2354-2361

  Thomsen, R ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; LIGANDS; OPTIMIZATION; STOCHASTIC SYSTEMS;

CONVERGENCE SPEED; DIFFERENTIAL EVOLUTION; DIFFERENTIAL EVOLUTION ALGORITHMS; EVOLUTIONARY ALGORITHMS (EAS); MOLECULAR DOCKING; OPTIMIZATION PROBLEMS; PROTEIN-LIGAND COMPLEXES; STOCHASTIC SEARCH METHODS;

EVOLUTIONARY ALGORITHMS;

EID: 84901429130     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CEC.2003.1299382     Document Type: Conference Paper

References (22)

1. H. M. Berman. J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig. I. N. Shindyalov. and RE. Bourne. The protein data bank. Nucleic Acids Research, Vol. 28, No. 1, pp. 235-242. 2000.
2. D. E. Clark, editor. Evolutionary Algorithms in Molecular Design. Wiley-VCH, 2000.
3. D. E. Clark and D. R. Westhead. Evolutionary algorithms in computer-aided molecular design. Journal of Computer-Aided Molecular Design, Vol. 10. pp. 337-358, 1996.
4. D. S. Goodsell and A. J. Olson. Automated docking of substrates to proteins by simulated annealing. PROTEINS: Structure, Function, and Genetics. Vol. 8, pp. 195-202, 1990.
5. W. E. Hart, C. Rosin. R. K. Belew. and G. M. Morris. Improved evolutionary hybrids for flexible ligand docking in autodock. In C. A. Floudas and P. M. Pardalos, editors, Optimization in Computational Chemistry and Molecular Biology, pp. 209-230, 2000.
6. G. Jones, P. Willett, R. C. Glen, A. R. Leach, and R. Taylor. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. Vol. 267, pp. 727-748, 1997.
7. S. Kirkpatrick, Jr. C. D. Gelatt, and M. P. Vecchi. Optimization by simulated annealing. Science. Vol. 220, No. 4598. pp. 671-680, 1983.
8. A. R, Leach. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol., Vol. 235, pp. 345-356, 1994.
9. N. Madavan. Multiobjective optimization using a pareto differential evolution approach. In David B. Fogel, Mohamed A. El-Sharkawi, Xin Yao, Garry Greenwood, Hitoshi Iba, Paul Marrow, and Mark Shackleton, editors, Proceedings of the 2002 Congress on Evolutionary Computation (CEC2002), pp. 1145-1150, 2002.
10. G. M. Morris, D. S. Goodsell. R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew, and A. J. Olson. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J. Comp. Chem., Vol. 19, No. 14, pp. 1639-1662. 1998.
11. G. M. Morris, D. S. Goodsell. R. Huey, W. E. Hart, S. Halliday, R. Belew, and A. J. Olson. AutoDock user's guide: Automated docking of flexible litgands to receptors, version 3.0.5. 2001.
12. G. M. Morris. D. S. Goodsell, R. Huey, and A. J. Olson. Distributed automated docking of flexible ligands to proteins: Parallel applications of autodock 2.4. Journal of Computer-Aided Molecular Design, Vol. 10, pp. 293-304, 1996.
13. K. Price and R. Storn. Differential evolution: A simple evolution strategy for fast optimization. Dr. Dobb's Journal of Software Tools, Vol. 22, No. 4, pp. 18-24, April 1997.
14. C. D. Rosin. R. Scott Halliday, W. E. Hart, and R. K. Belew. A comparison of global and local search methods in drug docking. In Proceedings of the 7th International Conference on Genetic Algorithms (ICGA-97), pp. 221-228, 1997.
15. F. Solis and R. Wets. Minimization by random search techniques. Math. Ops. Res., Vol. 6. pp. 19-30, 1981.
16. R. Storn. Designing digital filters with differential evolution. In David Covne, Marco Dorigo, and Fred Glover, editors, New Ideas in Optimization, pp. 109-125. McGraw-Hill, London, 1999.
17. R. Storn and K. Price. Differential evolution - a simple and efficient adaptive scheme for global optimization over continuous spaces. Technical Report TR-95-012, International Computer Science Institute, Berkley, 1995.
18. R. Storn and K, Price. Differential evolution a simple and efficient heuristic for global optimisation over continuous spaces. Journal of Global Optimization, Vol. 11, pp. 341-359, 1997.
19. P. F. W. Stouten, C. Frommel, H. Nakamura, and C. Sander. An effective solvation term based on atomic occupancies for use in protein simulations. Mol. Simulation, Vol. 10, pp. 97-120, 1993.
20. R. Thomsen. Flexible ligand docking using evolutionary algorithms: Investigating the effects of variation operators and local-search hybrids. Accepted for publication in BioSystems.
21. D. R. Westhead, D. E. Clark, and C. W. Murray. A comparison of heuristic search algorithms for molecular docking. Journal of Computer-Aided Molecular Design, Vol. 11, pp. 209-228, 1997.
22. J-M. Yang, J-T. Horng, and C-Y. Kao. Integrating adaptive mutations and family competition with differential evolution for flexible ligand docking. In Proceedings of the 2001 Congress on Evolutionary Computation (CEC200I), pp. 473-480, 2001.