Efficiency of tabu-search-based conformational search algorithms

Journal of Computational Chemistry

Volumn 32, Issue 10, 2011, Pages 2245-2253

  Grebner, Christoph ^a   Becker, Johannes ^a   Stepanenko, Svetlana ^a   Engels, Bernd ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

basin hopping; conformational search; global optimization; Monte Carlo with minimization; simulated annealing; Tabu search

Indexed keywords

BASIN HOPPING; BIOLOGICAL ACTIVITIES; CONFORMATIONAL SEARCH; CONFORMATIONAL SEARCH ALGORITHMS; MOLECULAR DYNAMICS METHODS; MONTE CARLO WITH MINIMIZATION; MULTIPLE RING; ORGANIC LIGANDS; RING STRUCTURES; SEARCH ALGORITHMS; SIMULATED ANNEALING METHOD; STRONG DEMAND;

EFFICIENCY; GLOBAL OPTIMIZATION; HYDROGEN; HYDROGEN BONDS; LEARNING ALGORITHMS; MOLECULAR DYNAMICS; SIMULATED ANNEALING; STRUCTURES (BUILT OBJECTS);

TABU SEARCH;

EID: 79958215566     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21807     Document Type: Article

References (98)

1. Goetschalckx, M.; Vidal, C. J.; Dogan, K., Eur J Oper Res 2002, 143, 1.
2. Kolda, T. G.; Lewis, R. M.; Torczon, V., SIAM Rev 2003, 45, 385.
3. Floudas, C. A.; Akrotirianakis, I. G.; Caratzoulas, S.; Meyer, C. A.; Kallrath, J., Comput Chem Eng 2005, 29, 1185.
4. Musafia, B.; Senderowitz, H., Exp Opin Drug Discov 2010, 5, 943.
5. Halperin, I.; Ma, B. Y.; Wolfson, H.; Nussinov, R., Proteins: Struct Funct Genet 2002, 47, 409.
6. Foloppe, N.; Chen, I. J., Curr Med Chem 2009, 16, 3381.
7. Wales, D. J.; Doye, J. P. K.; Miller, M. A.; Mortenson, P. N.; Walsh, T. R., In Advances in Chemical Physics, Prigione, I., Ed.; Vol. 115; John Wiley & Sons Inc: New York, 2000; pp. 1-111.
8. Wales, D. J.; Bogdan, T. V., J Phys Chem B 2006, 110, 20765.
9. Wales, D. J., Phys Biol 2005, 2, S86.
10. Wales, D. J., Int Rev Phys Chem 2006, 25, 237.
11. Becker, O. M.; MacKerrel, A. D., Jr.; Roux, B.; Watanabe, M., Computational Biochemistry and Biophysics; Marcel Dekker Inc.: New York, 2001.
12. Leach, A. R., Molecular Modelling-Principle and Application, 2nd ed.; Pearson Education Limited: Harlow, 2001.
13. Wales, J. D., Energy Landscapes; Cambridge University Press: United Kingdom, 2003.
14. Kannan, S.; Zacharias, M., J Struct Biol 2009, 166, 288.
15. Schlund, S.; Schmuck, C.; Engels, B., Chem Eur J 2007, 13, 6644.
16. Han, R. S.; Leo-Macias, A.; Zerbino, D.; Bastolla, U.; Contreras-Moreira, B.; Ortiz, A. R., Proteins: Struct Funct Bioinf 2008, 71, 175.
17. Lee, K., Int J Mol Sci 2008, 9, 65.
18. Leach, A. R., In Reviews in Computational Chemistry, Vol. 2;, Lipkowitz, K. B.; Boyd, D. B., Eds.; VCH: New York, 1991.
19. Senn, H. M.; Thiel, W., Angew Chem Int Ed Engl 2009, 48, 1198.
20. Engels, B.; Peyerimhoff, S. D., J Phys Chem 1989, 93, 4462.
21. Helten, H.; Schirmeister, T.; Engels, B., J Org Chem 2005, 70, 233.
22. Musch, P. W.; Engels, B., J Am Chem Soc 2001, 123, 5557.
23. Bruccoleri, R. E.; Karplus, M., Biopolymers 1987, 26, 137.
24. Gippert, G. P.; Wright, P. E.; Case, D. A., J Biomol NMR 1998, 11, 241.
25. Sadowski, J.; Bostrom, J., J Chem Inf Model 2006, 46, 2305.
26. Smellie, A.; Stanton, R.; Henne, R.; Teig, S., J Comput Chem 2003, 24, 10.
27. Chandrasekhar, J.; Saunders, M.; Jorgensen, W. L., J Comput Chem 2001, 22, 1646.
28. Chen, J. H.; Im, W.; Brooks, C. L., J Comput Chem 2005, 26, 1565.
29. Glen, R. C.; Payne, A. W. R., J Comput Aided Mol Des 1995, 9, 181.
30. Scheraga, H. A.; Lee, J.; Pillardy, J.; Ye, Y. J.; Liwo, A.; Ripoll, D., J Global Opt 1999, 15, 235.
31. Goodman, J. M.; Still, W. C., J Comput Chem 1991, 12, 1110.
32. Bohm, G., Biophys Chem 1996, 59, 1.
33. Floudas, C. A.; Klepeis, J. L.; Pardalos, P. M., DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 47; American Mathematical Society: New Jersey, 1999.
34. Neumaier, A., SIAM Rev 1997, 39, 407.
35. Li, Z. Q.; Laidig, K. E.; Daggett, V., J Comput Chem 1998, 19, 60.
36. Vengadesan, K.; Gautham, N., Curr Sci 2005, 88, 1759.
37. Kostrowicki, J.; Scheraga, H. A., J Phys Chem 1992, 96, 7442.
38. Chang, G.; Guida, W. C.; Still, W. C., J Am Chem Soc 1989, 111, 4379.
39. Morales, L. B.; Gardunojuarez, R.; Romero, D., J Biomol Struct Dynamics 1991, 8, 721.
40. Wilson, S. R.; Cui, W.; Moskowitz, J. W.; Schmidt, K. E., J Comput Chem 1991, 12, 342.
41. Grubmuller, H., Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 1995, 52, 2893.
42. Huber, T.; Torda, A. E.; van Gunsteren, W. F., J Comput Aided Mol Des 1994, 8, 695.
43. Iannuzzi, M.; Laio, A.; Parrinello, M., Phys Rev Lett 2003, 90, 238302.
44. Yang, Y. D.; Liu, H. Y., J Comput Chem 2006, 27, 1593.
45. Li, Z. G.; Scheraga, H. A., Biophys J 1987, 51, A232.
46. Li, Z. Q.; Scheraga, H. A., Proc Natl Acad Sci USA 1987, 84, 6611.
47. Wales, D. J.; Scheraga, H. A., Science 1999, 285, 1368.
48. Wales, D. J.; Doye, J. P. K., J Phys Chem A 1997, 101, 5111.
49. Hernandez-Rojas, J.; Breton, J.; Llorente, J. M. G.; Wales, D. J., J Phys Chem B 2006, 110, 13357.
50. Li, Z. Q.; Scheraga, H. A., Biophys J 1988, 53, A46.
51. Nanias, M.; Chinchio, M.; Oldziej, S.; Czaplewski, C.; Scheraga, H. A., J Comput Chem 2005, 26, 1472.
52. Oldziej, S.; Czaplewski, C.; Liwo, A.; Chinchio, M.; Nanias, M.; Vila, J. A.; Khalili, M.; Arnautova, Y. A.; Jagielska, A.; Makowski, M.; Schafroth, H. D.; Kazmierkiewicz, R.; Ripoll, D. R.; Pillardy, J.; Saunders, J. A.; Kang, Y. K.; Gibson, K. D.; Scheraga, H. A., Proc Natl Acad Sci USA 2005, 102, 7547.
53. Baumann, K.; von Korff, M.; Albert, H., J Chemom 2002, 16, 351.
54. Baumann, K.; Albert, H.; von Korff, M., J Chemom 2002, 16, 339.
55. Glover, F., ORSA J Comput 1989, 1, 190.
56. Glover, F., ORSA J Comput 1990, 2, 4.
57. Glover, F.; Laguna, M., Tabu Search; Kluwer Academic Publishers: MA, USA, 1997.
58. Blum, C.; Roli, A., ACM Computing Surveys 2003, 35, 268.
59. Pardalos, P. M.; Resende, M. G. C., Handbook of Applied Optimization; Oxford University Press: Oxford, 2002.
60. Rayward-Smith, V. J.; Osman, I. H.; Reeves, C. R.; Smith, G. D., Modern Heuristic Search Methods; Wiley: Chichester, 1996.
61. Ribeiro, C. C.; Hansen, P., Essays and Surveys in Metaheuristics; Kluwer Academic Publishers: Boston, MA, 2002.
62. Gendreau, M.; Potvin, J.-Y., Handbook of Metaheuristics, Vol. 146; Springer International Series in Operations Research & Management Science: New York, 2010.
63. Glover, F., Discrete Appl Math 1994, 49, 231.
64. Glover, F.; Mulvey, J. M.; Hoyland, K., In Meta-Heuristics: Theory & Applications;, Osman, I. H., Kelly, J. P., Eds.; Kluwer Academic Publishers: Berlin, 1996; pp. 429-448.
65. Hvattum, L. M.; Glover, F., Eur J Oper Res 2009, 195, 31.
66. Ugray, Z.; Lasdon, L.; Plummer, J.; Glover, F.; Kelly, J.; Marti, R., Informs J Comput 2007, 19, 328.
67. Duarte, A.; Marti, R.; Glover, F.; Gortazar, F., In Annals of Operations Research; Springer Science+Business Media, LLC: Piscataway, New Jersey, 2009.
68. Stepanenko, S.; Engels, B., J Comput Chem 2007, 28, 601.
69. Stepanenko, S.; Engels, B., J Comput Chem 2008, 29, 768.
70. Stepanenko, S.; Engels, B., J Phys Chem A 2009, 113, 11699.
71. Dennis, J. E.; Schnabel, R. B., Numerical Methods for Unconstrained Optimization; SIAM: Philadelphia, 1996.
72. Gill, P. E.; Murray, W.; Wright, M. H., Practical Optimization; Academic Press: San Diego, 1981.
73. Nocedal, J.; Wright, S. J., Numerical Optimization; Springer: New York, 1999.
74. Press, W. H.; Teukolsky, S. A.; Vetterling, W. T.; Flannery, B. P., Numerical Recipes in C++, 2nd ed.; Cambridge University Press: New York, 2002.
75. Bogdan, T. V.; Wales, D. J.; Calvo, F., J Chem Phys 2006, 124, 044102.
76. Kirchner, B., J Chem Phys 2005, 123, 204116.
77. Kryshtafovych, A.; Fidelis, K., Drug Discov Today 2009, 14, 386.
78. Abagyan, R.; Totrov, M.; Kuznetsov, D., J Comput Chem 1994, 15, 488.
79. Baysal, C.; Meirovitch, H., J Chem Phys 1996, 105, 7868.
80. Felts, A. K.; Gallicchio, E.; Chekmarev, D.; Paris, K. A.; Friesner, R. A.; Levy, R. M., J Chem Theory Comput 2008, 4, 855.
81. Náray-Szabõ, G.; Warshel, A., Computational Approaches to Biochemical Reactivity; 1st ed.; Kluwer Academic Publisher: New York, 2002.
82. Qu, X. T.; Swanson, R.; Day, R.; Tsai, J., Curr Protein Pept Sci 2009, 10, 270.
83. Wei, B. Q.; Weaver, L. H.; Ferrari, A. M.; Matthews, B. W.; Shoichet, B. K., J Mol Biol 2004, 337, 1161.
84. Xia, J. C.; Margulis, C., J Biomol NMR 2008, 42, 241.
85. Zhang, Y., Curr Opin Struct Biol 2008, 18, 342.
86. Clayden, J.; Greeves, N.; Warren, S.; Wothers, P., Organic Chemistry; Oxford University Press: New York, 2004.
87. Abagyan, R. A.; Mazur, A. K., J Biomol Struct Dynamics 1989, 6, 833.
88. Mazur, A. K.; Abagyan, R. A., J Biomol Struct Dynamics 1989, 6, 815.
89. Echenique, P.; Alonso, J. L., J Comput Chem 2006, 27, 1076.
90. Ponder, J. W.; Richards, F. M., J Comput Chem 1987, 8, 1016.
91. Hodsdon, M. E.; Ponder, J. W.; Cistola, D. P., J Mol Biol 1996, 264, 585-602.
92. Kundrot, C. E.; Ponder, J. W.; Richards, F. M., J Comput Chem 1991, 12, 402.
93. Pappu, R. V.; Hart, R. K.; Ponder, J. W., J Phys Chem B 1998, 102, 9725.
94. Ren, P. Y.; Ponder, J. W., J Comput Chem 2002, 23, 1497.
95. Ren, P. Y.; Ponder, J. W., J Phys Chem B 2003, 107, 5933.
96. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J., J Am Chem Soc 1996, 118, 11225.
97. Evans, D. A.; Wales, D. J., J Chem Phys 2003, 119, 9947-9955.
98. Lee, J.; Scheraga, H. A.; Rackovsky, S., J Comput Chem 1997, 18, 1222.