A new hybrid algorithm for finding the lowest minima of potential surfaces: Approach and application to peptides

Journal of Computational Chemistry

Volumn 32, Issue 9, 2011, Pages 1785-1800

  Goldstein, Moshe ^a,b   Fredj, Erick ^b   Gerber, R Benny ^a,c  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b JERUSALEM COLLEGE OF TECHNOLOGY   (Israel)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

cyclic peptides; diffusion equation method; evolutionary programming; hybrid algorithm; simulated annealing; structure prediction

Indexed keywords

CYCLIC PEPTIDES; DIFFUSION EQUATION METHOD; EVOLUTIONARY PROGRAMMING; HYBRID ALGORITHM; STRUCTURE PREDICTION;

COMPUTATIONAL EFFICIENCY; COMPUTER PROGRAMMING; DIFFUSION; FORECASTING; GLOBAL OPTIMIZATION; MACROS; PARTIAL DIFFERENTIAL EQUATIONS; PEPTIDES; QUANTUM CHEMISTRY; SIMULATED ANNEALING;

EVOLUTIONARY ALGORITHMS;

PEPTIDE;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION;

EID: 79955480270     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21755     Document Type: Article

References (93)

1. Petsko, G. A.; Ringe, D., Protein Structure and Function; New Science Press Ltd. UK, Available at, 2007.
2. Leach, A., Molecular Modelling-Principles and Applications, 2nd ed.; Prentice-Hall: England, 2001.
3. Schlick, T., Molecular Modeling and Simulation-An Interdisciplinary Guide; Springer-Verlag: USA, 2002.
4. Finkelstein, A. V., Curr Opin Struct Biol 1997, 7, 60-71.
5. Nolting, B., Protein Folding Kinetics-Biophysical Methods, 2nd ed.; Springer-Verlag: Germany, 2006.
6. Prentiss, M. C.; Hardin, C.; Eastwood, M. P.; Zong, Ch.; Wolynes, P.G., J Chem Theory Comput 2006, 2, 705-716.
7. Finkelstein, A. V.; Galzitskaya, O. V., Phys Life Rev 2004, 1, 23-56.
8. Helling, R.; Li, H.; Melin, R.; Miller, J.; Wingree, N.; Zeng, Ch.; Tang, Ch., J Mol Graph Model 2001, 19, 157-167.
9. Honig, B., J Mol Biol 1999, 293, 283-293.
10. Karplus, M., Fold Des 1997, 2, S69-S75.
11. Dobson, C. M.; Karplus, M., Curr Opin Struct Biol 1999, 9, 92-101.
12. Dinner, A. R.; Sali, A.; Smith, L. J.; Dobson, Ch. M.; Karplus, M., Trends Biochem Sci 2000, 25, 331-339.
13. Goodman, J. M., Chemical Applications of Molecular Modeling; The Royal Society of Chemistry: UK, 1998.
14. Cramer, Ch. J., Essentials of Computational Chemistry-Theories and Models; Wiley: England, 2002.
15. Ponder, J. W.; Case, D. A., Adv Prot Chem 2003, 66, 27-85.
16. Lazaridis, Th.; Karplus, M., Curr Opin Struct Biol 2000, 10, 139-145.
17. Neumaier, A., SIAM Rev 1997, 39, 407-460.
18. Floudas, C. A.; Klepeis, J. L.; Pardalos, P. M., Proc DYCOPS-5, 1998, 167-178.
19. Krieger, E.; Nabuurs, S. B.; Vriend, G., Structural Bioinformatics; Wiley-Liss Inc.: USA, 2003; pp. 507-521.
20. Zhang, Y.; Skolnik, J., PNAS 2005, 102, 1029-1034.
21. Bonneau, R.; Baker, D., Annu Rev Biophys Biomol Struct 2001, 30, 173-189.
22. Rohl, C. A.; Strauss, Ch. E. M.; Misura, K. M. S.; Baker, D., Methods Enzymol 2004, 383, 66-93.
23. Chaban, G. M.; Jung, J. O.; Gerber, R. B., J Phys Chem 2000, 104, 10035-10044.
24. Chaban, G. M.; Gerber, R. B., J Chem Phys 2001, 115, 1340-1348.
25. Gerber, R. B.; Chaban, G. M.; Gregurick, S. K.; Brauer, B., Biopolymers 2003, 68, 370-382.
26. Goldberg, D. E.; Voessner, S., In Proceedings of the GECCO′99, 1999; pp. 220-228.
27. Sinha, A.; Goldberg, D. E., In Proceedings of the GECCO′01, 2001; pp. 592-598.
28. Sinha, A.; Goldberg, D. E., IlliGAL Report No. 2003004, 2003.
29. Talbi, E.-G. A., J Heu 2002, 8, 541-564.
30. Grosan, C.; Abraham, A., Comput Intell 2007, 75, 1-7.
31. Krasnogor, N.; Smith, J., IEEE T Evol Comput 2005, 9, 474-488.
32. Michalewicz, Z.; Fogel, D. B., How to Solve It: Modern Heuristics; Springer-Verlag: Germany, 2000.
33. Eiben, A. E.; Smith, J. E., Introduction to Evolutionary Computing; Springer-Verlag: Germany, 2007.
34. Back, T.; Fogel, D. B.; Michalewicz, T., Eds. Evolutionary Computation 1: Basic Algorithms and Operators; IOP Publishing Ltd.: UK, 2000.
35. Ponder, J. W., TINKER: Software Tools for Molecular Design, Version 4.1, Washington University School of Medicine, 2003.
36. Fogel, L. J., On the Organization of Intellect; PhD Dissertation, UCLA, 1964.
37. Fogel, L. J.; Owens, A. J.; Walsh, M. J., Artificial Intelligence Through Simulated Evolution; Wiley: USA, 1966.
38. Piela, L.; Kostrowicki, J.; Scheraga, H. A., J Phys Chem 1989, 93, 3339-3346.
39. Kostrowicli, J.; Scheraga, H. A., J Phys Chem 1992, 96, 7442-7449.
40. Scheraga, H. A.; Lee, J.; Pillardy, J.; Ye, Y.-J.; Liwo, A.; Ripoll, D. J., Global Opt 1999, 15, 235-260.
41. Straub, J. E., New Developments in Theoretical Studies of Proteins, World Scientific Publication: Singapore, 1996; pp. 137-196.
42. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P., Science 1983, 220, 671-680.
43. Yao, X., Int J Comp Math 1991, 40, 169-189.
44. Eiben, A. E.; Schippers, C. A., Fundam Inform 1998, 35, 1-16.
45. Liu, D. C.; Nocedal, J., Math Program 1989, 45, 503-528.
46. Lee, Ch.-Y.; Yao, X., IEEE T Evol Comput 2004, 8, 1-13.
47. Kolinski, A.; Skolnick, J., Polymer 2004, 45, 511-524.
48. Clementi, C., Curr Opin Struct Biol 2007, 17, 1-6.
49. Nakamura, Sh.; Hirose, H.; Ikeguchi, M.; Doi, J., J Phys Chem 1995, 99, 8374-8378.
50. Pappu, R. V.; Hart, R. K.; Ponder, J. W., J Phys Chem B 1998, 102, 9725-9742.
51. Hart, R. K.; Pappu, R. V.; Ponder, J. W., J Comp Chem 2000, 21, 531-552.
52. Hill, R. R., In: Proceedings of the 31st WSC, 1999; pp. 543-547.
53. Ursem, R. K., PPSN VII, LNCS 2436, 2002, 462-471.
54. Morrison, R. W., GECCO-2003 LNCS 2723; Springer-Verlag: Germany, 2003; pp. 1210-1221.
55. Nguyen, D. H. M.; Wong, K. P., In: Proceedings of the 2nd ICMLC, 2003; pp. 775-780.
56. Rahnamayan, Sh.; Tzihoosh, H. R.; Salama, M. M. A., CAMWA 2007, 53, 1605-1614.
57. Maaranen, H.; Miettinen, K.; Penttinen, A., J Global Opt 2007, 37, 405-436.
58. Cui, Q.; Ivet Bahar, I., Eds., Normal Mode Analysis-Theory and Applications to Biological and Chemical Systems; Chapman & Hall/CRC: USA, 2006.
59. Thierens, D., In: Proceedings of the 7th ICGA, 1997; pp. 152-159.
60. Thierens, D.; Goldberg, D., In: Proceedings of the 1st ICEC, 1994; pp. 508-512.
61. Koakutsu, S.; Kang, M.; Dai, W. W., In: Proceedings of the 5th ACM/SIGDA PDW, 1996; pp. 134-141.
62. Back, T.; Fogel, D. B.; Michalewicz, T., Eds. Evolutionary Computation 2: Advanced Algorithms and Operators; IOP Publishing Ltd.: UK, 2000.
63. Meyer-Nieberg, S.; Beyer, H.-G., Stud Comp Intell 2007, 54, 47-75.
64. Liang, K.-H.; Yao, X.; Newton, Ch. S., Appl Intell 2001, 15, 171-180.
65. Herrera, F.; Lozano, M., Appl Intell 2000, 13, 187-204.
66. Saravanan, N.; Fogel, D. B.; Nelson, K. M., BioSystems 1995, 36, 157-166.
67. Eiben, A. E.; Schutt, M. C.; de Wilde, A. R., 2006 IEEE C Evol Comput 2006, 1584-1589.
68. Reeves, C. R., In: Proceedings of the 5th ICGA, 1993; pp. 92-99.
69. Ghosh, A.; Tsutsui, Sh.; Tanaka, H.; Corne, D., KES J 2000, 4, 64-71.
70. Kazarlis, S. A.; Papadakis, S. E.; Theocharis, J. B.; Petridis, V., IEEE Trans Evol Comput 2001, 5, 204-217.
71. Tian, Y.; Qian, J.; Meng, F., PIERS 2005, 1, 101-104.
72. Koumousis, V. K.; Katsaras, Ch. P., IEEE Trans Evol Comput 2006, 10, 19-28.
73. Aytug, H.; Koehler, G. J., Eur J Oper Res 2000, 126, 662-674.
74. Hernandez, G.; Wilder, K.; Nino, F.; Garcia, J., In: Proceedings of the GECCO′05, 2005; pp. 615-620.
75. Zielinski, K.; Laur, R., Informatica 2007, 31, 51-59.
76. Pendharkar, P. C.; Koehler, G. J., Eur J Oper Res 2007, 176, 1436-1451.
77. Martelli, A., Python in a Nutshell-A Desktop Quick Reference; O'Reilly & Associates Inc.: USA, 2003.
78. Barak, A.; Shiloh, A., The MOSIX Management System for Linux Clusters, GPU Clusters and Clouds, a white paper, 2008. Available at.
79. Rayan, A.; Senderowitz, H.; Goldblum, A., J Mol Graph Mod 2004, 22, 319-333.
80. Yang, Ch.-H.; Brown, J. N.; Kopple, K. D., J Am Chem Soc 1981, 103, 1715-1719.
81. Kopple, K. D; Go, A.; Logan, R. H., Jr.; Savrda, J., J Am Chem Soc 1972, 94, 973-981.
82. Pettit, G. R.; Cichacz, Zb.; Barkoczy, J.; Dorsaz, A.-Ch.; Herald, D. L.; Williams, M. D.; Doubek, D. L.; Schmidt, J. M.; Tackett, L. P.; Brune, D. C.; Cerny, R. L.; Hooper, J. N. A.; Bakus, G. J., J Nat Prod 1993, 56, 260-267.
83. Pettit, G. R.; Srirangam, J. K.; Herald, D. L.; Erickson, K. L.; Doubek, D. L.; Schmidt, J. M.; Tackett, L. P.; Bakus, G. J., J Org Chem 1992, 57, 7217-7220.
84. Eggleston, D. S.; Baures, P. W.; Peishoff, C. E.; Kopple, K. D., J Am Chem Soc 1991, 113, 4410-4416.
85. Peisboff, C. E.; Bean, J. W.; Kopple, K. D., J Am Chem Soc 1991, 113, 4416-4421.
86. Jorgensen, W. L.; Tirado-Rives, J., J Am Chem Soc 1988, 110, 1657-1666.
87. Siew, N.; Elofsson, A.; Rhychlewski, L.; Fischer, D., Bioinformatics 2000, 16, 776-785.
88. Herbert, A., MaxCluster-A tool for Protein Structure Comparison and Custering, 2008. Available at.
89. Zemla, A., Nucl Acids Res 2003, 31, 3370-3374.
90. Zhang, Y.; Skolnick, J., Nucl Acids Res 2005, 33, 2302-2309.
91. Ortiz, A. R.; Strauss, Ch. E. M.; Olmea, O., Protein Sci 2002, 11, 2606-2621.
92. Feig, M.; Brooks, Ch. L., III,. Curr Opin Struct Biol 2004, 14, 217-224.
93. Im, W.; Chen, J.; Brooks, Ch. L., III,. Adv Protein Chem 2006, 72, 173-198.