A grid-based genetic algorithm combined with an adaptive simulated annealing for protein structure prediction

Soft Computing

Volumn 12, Issue 12, 2008, Pages 1185-1198

  Tantar, Alexandru Adrian ^a   Melab, Nouredine ^a   Talbi, El Ghazali ^a  

^a ECOLE CENTRALE DE LILLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE ALGORITHMS; ALGORITHMS; AMINO ACIDS; ANNEALING; CHLORINE COMPOUNDS; COMPUTATIONAL COMPLEXITY; COMPUTER SYSTEMS; EVOLUTIONARY ALGORITHMS; FORECASTING; GENETIC ALGORITHMS; GRID COMPUTING; HEURISTIC PROGRAMMING; MULTIOBJECTIVE OPTIMIZATION; PARALLEL ALGORITHMS; PARALLEL PROCESSING SYSTEMS;

ADAPTIVE SIMULATED ANNEALING; ADMINISTRATIVE DOMAINS; BIO-INSPIRED; COMPUTATIONAL GRIDS; CONJUGATED GRADIENT; CYCLO DEXTRIN; EXPLORATION PROCESS; GRID ENVIRONMENTS; GRID INFRASTRUCTURES; HYBRID MODEL; LOCAL SEARCH METHODS; META-HEURISTICS; MULTI-START; PARALLEL COMPUTING; PARALLEL EVALUATION; PARALLELIZATION; PROTEIN DATA BANK; PROTEIN STRUCTURE PREDICTION;

SIMULATED ANNEALING;

EID: 49149109393     PISSN: 14327643     EISSN: 14337479     Source Type: Journal    
DOI: 10.1007/s00500-008-0298-8     Document Type: Article

References (44)

1. Alba E, Luque G, Talbi E-G, Melab N (2005) Metaheuristics and parallelism. In: Alba E (ed) PaAellel metaheuristics: a new class of algorithms, Chap. 4. Wiley Series on Parallel and Distributed Computing. Wiley, New Jersey, pp 79-104. ISBN 0-471-67806-6
2. Alder BJ, Wainwright TE (1957) Phase transition for a hard sphere system. J Chem Phys 27: 1208
3. Alder BJ, Wainwright TE (1959) Studies in molecular dynamics I: General method. J Chem Phys 31: 459
4. Bernstein FC, Koetzle TF, Williams GJ, Meyer E, Bryce MD, Rogers JR, Kennard O, Shikanouchi T, Tasumi M (1977) The protein data bank: A computer-based archival file for macromolecular structures. J Mol Biol 112: 535-542
5. Bolze R, Cappello F, Caron E, Dayde M, Desprez F, Jeannot E, Jegou Y, Lanteri S, Leduc J, Melab N, Mornet G, Namyst R, Primet P, Quetier B, Richard O, Talbi E-G, Touche I (2006) Grid'5000: A large scale and highly reconfigurable experimental grid testbed. Int J High Performance Comput Appl 20(4): 481-494
6. Bonneau R, Tsui J, Ruczinski I, Chivian D, Strauss CME, Baker D (2001) Rosetta in CASP4: Progress in ab-initio protein structure prediction. Proteins 45: 119-126
7. Calland P-Y (2003) On the structural complexity of a protein. Protein Eng 16(2): 79-86
8. Cahon S, Melab N, Talbi E-G (2004) ParadisEO: A framework for the reusable design of parallel and distributed metaheuristics. J Heuristics 10: 357-380
9. Cahon S, Melab N, Talbi E-G (2005) An enabling framework for parallel optimization on the computational grid. In: Proceedings of 5th IEEE/ACM international symposium on cluster computing and the grid (CCGRID'2005), Cardiff, 9-12 May
10. Crescenzi P, Goldman D, Papadimitriou CH, Piccolboni A, Yannakakis M (1998) On the complexity of protein folding. J Comput Biol 5(3): 423-466
11. Dorsett H, White A (2000) Overview of molecular modelling and ab initio molecular orbital methods suitable for use with energetic materials. Department of Defense, Weapons Systems Division, Aeronautical and Maritime Research Laboratory, DSTO-GD-0253, Salisbury South Australia, September
12. Holland JH (1975) Adaptation in natural and artificial systems. University of Michigan Press, Ann Arbor
13. Ingber L (1993a) Adaptive simulated annealing (ASA), global optimization C-code, Caltech Alumni Association
14. Ingber L (1993b) Simulated annealing: Practice versus theory. Math Comput Model 11(18): 29-57
15. Ingber L (1996) Adaptive simulated annealing (ASA): Lessons learned. Control Cybern 25(1): 33-54
16. Ingber L (2001) Adaptive Simulated Annealing (ASA) and Path- Integral (PATHINT) algorithms: Generic tools for complex systems, ASA-PATHINT Lecture Plates, Lester Ingber Research
17. Ingber L, Rosen B (1993) Genetic algorithms and very fast simulated reannealing: A comparison. Oper Res Manage Sci 5(33): 523
18. Islas AL, Schober CM (2003) Multi-symplectic integration methods for generalized Schrödinger equations. Future Generation Comput Syst 19: 403-413
19. Kikuchi H, Kalia RK, Nakano A, Vashishta P, Iyetomi H, Ogata S, Kouno T, Shimojo F, Tsuruta K, Saini S (2002) Collaborative simulation grid: multiscale quantum-mechanical/classical atomistic simulations on distributed PC clusters in the US and Japan. IEEE, New York
20. Krasnogor N, Hart W, Smith J, Pelta D (1999) Protein structure prediction problem with evolutionary algorithms. In: Proceedings of the genetic and evolutionary computation conference
21. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220(4598): 671-680
22. Lattman EE (2001) CASP. Proteins 4(44): 399
23. Levinthal C (1969) Mossbauer spectroscopy in biological systems. In: DeBrunner JTP, Munck E (eds) Proc. How to Fold Graciously). University of Illinois Press, proceedings of a meeting held at Allerton House, Monticello, pp 22-24
24. McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature (Lond.) 267(5612): 585-590
25. Melab N, Cahon S, Talbi E-G (2006) Grid computing for parallel bioinspired algorithms. J Parallel Distrib Comput (JPDC) 66(8): 1052-1061
26. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21(6): 1087-1092. doi: 10.1063/1.1699114
27. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1999) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662
28. Moore BE, Reich S (2003) Multi-symplectic integration methods for Hamiltonian PDEs. Future Generation Syst 19: 395-402
29. Nakano A, Kalia RK, Vashishta P, Campbell TJ, Ogata S, Shimojo F, Saini S (2001) Scalable atomistic simulation algorithms for materials research. SC2001 November 2001, Denver (c) 2001. ACM, New York
30. Neumaier A (1997) Molecular modelling of proteins and mathematical prediction of protein structure. SIAM Rev 39: 407-460
31. Ngo JT, Marks J (1992) Computational Complexity of a Problem in Molecular-Structure Prediction. Protein Eng 5(4): 313-321
32. Pant A, Jafri H (2004) Communicating efficiently on cluster based grids with MPICH-VMI. In: 2004 IEEE International Conference on Cluster Computing (CLUSTER'04), pp 23-33
33. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612
34. Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66: 27-85
35. Rabow A, Scheraga H (1996) Protein. Science 5: 1800-1815
36. Sherwood P (2000) Hybrid quantum mechanics/molecular mechanics approaches, modern methods and algorithms of quantum chemistry, proceedings, 2nd edn. In: Grotendorst J (ed) John von Neumann Institute for Computing, Jülich, NIC Series, vol 3. ISBN 3-00-005834-6, pp 285-305
37. Tantar A-A, Melab N, Talbi E-G, Toursel B (2006) Solving the protein folding problem with a bicriterion genetic algorithm on the grid. CCGRID, Vol. 2, ISBN 0-7695-2585-7, 43, 2006
38. Tantar A-A, Melab N, Talbi E-G, Parent B, Horvath D (2007) A parallel hybrid genetic algorithm for protein structure prediction on the computational grid. Future Generation Comput Syst 23: 398-409
39. Talbi E-G (2002) A taxonomy of hybrid metaheuristics. J Heuristics 8: 541-564
40. Thomsen R (2003) Flexible ligand docking using evolutionary algorithms: investigating the effects of variation operators and local search hybrids. Biosystems 72: 57-73
41. Vande Waterbeemd H, Carter RE, Grassy G, Kubinyi H, Martin YC, Tute MS, Willett P (1997) Glossary of terms used in computational drug design. Pure Appl Chem 69(5): 1137-1152
42. Vreven T, Morokuma K, Farkas Ö, Schlegel HB, Frisch MJ (2003) Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints. Wiley Periodicals Inc. J Comput Chem 24: 760-769
43. Westhead DR, Clark DE, Murray CW (1997) A comparison of heuristic search algorithms for molecular docking. J Comput Aided Molec Des 11: 209-228
44. White A, Zerilli FJ, Jones HD (2000) Ab initio calculation of intermolecular potential parameters for gaseous decomposition products of energetic materials. Department of Defense, Energetic Materials Research and Technology Department, Naval Surface Warfare Center, DSTO-TR-1016, Melbourne Victoria 3001 Australia, August