On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

Journal of Computational Chemistry

Volumn 29, Issue 2, 2008, Pages 157-166

  Christen, Markus ^a   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Ensembles; Molecular dynamics; Monte Carlo; Sampling; Searching; Trajectories

Indexed keywords

CONFORMATIONS; DEGREES OF FREEDOM (MECHANICS); MOLECULAR DYNAMICS; MONTE CARLO METHODS; POTENTIAL ENERGY; THERMODYNAMIC PROPERTIES;

BIOMOLECULAR SYSTEMS; BOLTZMANN-WEIGHTED ENSEMBLES; CLASSICAL-DYNAMICAL TRAJECTORIES; CONFORMATIONAL SPACE;

BIOMOLECULES;

ALGORITHM; ARTICLE; BIOTECHNOLOGY; COMPUTER SIMULATION; CONFORMATION; ENERGY TRANSFER; METHODOLOGY; THERMODYNAMICS;

ALGORITHMS; BIOTECHNOLOGY; COMPUTER SIMULATION; ENERGY TRANSFER; MOLECULAR CONFORMATION; THERMODYNAMICS;

EID: 37649014404     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20725     Document Type: Article

References (165)

1. Rice, L. M.; Brünger, A. T. Proteins 1994, 19, 277.
2. Güntert,P.;Mumenthaler,C.; Wüthrich, K. J Mol Biol 1997, 273, 283.
3. Schäfer, M.; Bartels, C.; Karplus, M. J Mol Biol 1998, 284, 835.
4. Zhang, L. Y.; Gallicchio, E.; Friesner,R. A.; Levy, R. M. J Comp Chem 2001, 22, 591.
5. Daura, X.; Mark, A. E.; van Gunsteren, W. F. Comput Phys Commun 1999, 123, 97.
6. van der Vegt, N. F. A.; Trzesniak, D.; Kasumaj, B.; van Gunsteren, W. F. Chem Phys Chem 2004, 5, 144.
7. Schuler, L. D.; van Gunsteren, W. F. Mol Simul 2000, 25, 301.
8. Oostenbrink, C.; Juchli, D.; van Gunsteren, W. F. Chem Phys Chem 2005,6, 1800.
9. Smit, B.; Hilbers, P. A. J.; Esselink, K.; Rupert, L. A. M.; van Os, N. M.; Schlijper, A. J. Nature 1990, 348, 624.
10. Baschnagel, J.; Binder, K.; Doruker, P.; Gusev, A. A.; Hahn, O.; Kremer, K.; Mattice, W. L.; Müller-Plathe, F.; Murat, M.; Paul, W.; Santos, S.; Suter, U.W.; Tries, V. Adv Polymer Sci 2000, 152, 41.
11. Shelley, J. C.; Shelley, M. Y. Curr Opin Colloid Interface Sci 2000, 5, 101.
12. Müller, M.; Katsov, K.; Schick, M. J Polym Sci Part B: Polym Phys 2003, 41, 1441.
13. Tozzini, V. Curr Opin Struct Biol 2005, 15, 144.
14. Lwin, T. Z.; Luo, R. J Chem Phys 2005, 123, 194904.
15. Christen, M.; van Gunsteren, W. F. J Chem Phys 2006, 124, 154106.
16. van Gunsteren, W. F.; Karplus, M. Macromolecules 1982, 15, 1528.
17. Katz, H.; Walter, R.; Somorjay, R. L. Comput Chem 1979, 3, 25.
18. Mazur, A. K.; Dorofeev, V. E.; Abagyan, R. A. J Comput Phys 1991, 92, 261.
19. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327.
20. Ciccotti, G.; Ferrario, M.; Ryckaert, J.-P. Mol Phys 1982, 47, 1253.
21. Wittenburg, J. Dynamics of Systems of Rigid Bodies; Teubner: Stuttgart, 1977.
22. Bae, D. S.; Haug, E. J. Mech Struct Mach 1987, 15, 359.
23. Bae, D. S.; Haug, E. J. Mech Struct Mach 1988, 15, 481.
24. Jain, A.; Vaidehi, N.; Rodriguez, G. J Comput Phys 1993, 106, 258.
25. Mathiowetz, A. M.; Jain, A.; Karasawa, N.; Goddard, W. A. III, Proteins 1994, 20, 227.
26. Stocker, U.; Juchli, D.; van Gunsteren, W. F. Mol Simul 2003, 29, 123.
27. Reich, S. Physica D 1995, 89, 28.
28. Zhou, J.; Reich, S.; Brooks, B. R. J Chem Phys 2000, 112, 1919.
29. Christen, M.; van Gunsteren, W. F. J Chem Phys 2005, 122, Art. No. 144106.
30. van Gunsteren, W. F.; Berendsen, H. J. C. Angew Chem Int Ed 1990, 29, 992.
31. Desmet, J.; DeMaeyer, M.; Hazes, B.; Lasters, I. Nature 1992, 356, 539.
32. Lipton, M.; Still, W. C. J Comput Chem 1988, 9, 343.
33. Bensen, D. D.; Marshall, G. R. In Protein Structure and Engineering; Jardetzky, O., Ed., Plenum: New York, 1989. NATO ASI Series A183, pp. 97-109.
34. Saunders, M.; Houk, K. N.; Wu, Y D.; Still, W. C.; Lipton, M.; Chang, G.; Guida, W. C. J Am Chem Soc 1990, 112, 1419.
35. Covell, D. G.; Jernigan, L. Biochem 1990, 29, 3287.
36. Ngo, J. T.; Karplus, M. J Am Chem Soc 1997, 119, 5657.
37. Crippen, G. M.; Havel, T. F. Distance Geometry and Molecular Conformation; Wiley: New York, 1988.
38. Havel, T. F. Biopolymers 1990, 29, 1565.
39. Jones, D. T.; Thornton, J. M. J Comp-Aided Mol Design 1993,7, 439.
40. Jones, D. T.; Miller, R. T.; Thornton, J. M. Proteins 1995, 23, 387.
41. Hamprecht, F. A.; Scott, W. R. P.; van Gunsteren, W. F. Proteins 1997, 28, 522.
42. Gibson, K. D.; Scheraga, H. A. J Comput Chem 1987, 8, 826.
43. Scheraga, H. A. In Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, Vol. 7; van Gunsteren, W. F; Weiner, P. K.; Wilkinson, A. J., Escom Science Publishers: Leiden, The Netherlands, 1993; pp. 231-248.
44. Vajda, S.; Delisi, C. Biopolymers 1990, 29, 1755.
45. Harris, J.; Rice, S. A. J Chem Phys 1988, 88, 1298.
46. Velikson, B.; Garel, T.; Niel, J.-C.; Orland, H.; Smith, J. C. J Comput Chem 1992, 13, 1216.
47. Frenkel, D.; Mooij, G. C. A. M.; Smit, B. J Phys Condens Matter 1992, 4, 3053.
48. van Gunsteren, W. F. In Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, Vol. 2; van Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A. J., Eds.; Escom Science Publishers: Leiden, The Netherlands, 1993; pp. 3-36.
49. Pangali, C.; Rao, M.; Berne, B. J. Chem Phys Lett 1978, 55, 413.
50. Cotterill, R. M. J.; Madsen, J. K. In Characterising Complex Systems; Bohr, H., Ed.; World Scientific, Singapore, 1990; pp. 177-191.
51. Byrne, D.; Li, J.; Piatt, E.; Robson, B.;Weiner, P. J Comput-Aided Mol Des 1994, 8, 67.
52. van Schaik, R. C.; van Gunsteren, W. F.; Berendsen, H. J. C.; J of Computer-Aided Mol Design 1992, 6, 97.
53. Stolovitzky, G.; Berne, B. J. Proc Natl Acad Sci U.S.A. 2000, 97, 11164.
54. Torda, A. E.; Scheek, R. M.; van Gunsteren, W. F. Chem Phys Lett 1989, 157, 289.
55. Wu, X. W.; Wang, S. M. J Phys Chem B 1998, 102, 7238.
56. Wu, X. W.; Wang, S. M. J Chem Phys 1999, 110,9401.
57. Andricioaei, I.; Dinner, A. R.; Karplus, M. J Chem Phys 2003, 118, 1074.
58. Wu, X. W.; Brooks, B. R. Chem Phys Lett 2003, 381, 512.
59. van Gunsteren, W. F.; Huber, T.; Torda, A. E. In Proceedings of European Conference on Computational Chemistry (E.C.C.C 1), Vol. 330; American Institute of Physics (A.I.P.), 1995; pp. 253-268.
60. van Gunsteren, W. F.; Berendsen, H. J. C.; Colonna, F.; Perahia, D.; Hollenberg, J. P.; Lellouch, D. J Comput Chem 1984, 5, 272.
61. Heinz, T N.; Hünenberger, P H. J Comput Chem 2004, 25, 1474.
62. Hockney, R. W.; Eastwood, J. W. Computer Simulation Using Particles, 2nd ed.; Institute of Physics Publishing: Bristol, 1988.
63. Luty, B. A.; Davis, M. E.; Tironi, I. G.; van Gunsteren, W. F. Mol Simul 1994, 14, 11.
64. Peter, C.; van Gunsteren, W. F.; Hünenberger, P. H. J Chem Phys 2003, 119, 12205.
65. Barker, J. A.; Watts, R. O. Mol Phys 1973, 26, 789.
66. Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. J Chem Phys 1995, 102, 5451.
67. Teleman, O.; Jonsson, B.; J Comput Chem 1986, 7, 58.
68. Tuckerman, M. E.; Martyna, G. J. J Chem Phys 1992, 97, 1990.
69. Watanabe, M.; Karplus, M.; J Chem Phys 1993, 99, 8063.
70. Izaguirre, J. A.; Reich, S.; Skeel, R. J Chem Phys 1999, 110, 9853.
71. Chun, H. M.; Padilla, C. E.; Chin, D. N.; Watanabe, M.; Karlov, V I.; Alper, H. E.; Soosar, K.; Blair, K. B,; Becker, O. M.; Caves, L. S. D.; Nagle, R.; Haney, D. N.; Farmer, B. L. J Comput Chem 2000, 21, 159.
72. Kräutler, V.; Hünenberger, P H. J Comput Chem 2006, 27, 1163.
73. Covell, D. G.; Jernigan, R. L. Biochemistry 1990, 29, 3287.
74. Skolnick, J.; Kolinski, A. Science 1990, 250, 1121.
75. van Gunsteren, W. F. In Advances in Biomolecular Simulations, Vol. 239; Lavery, R.; Rivail, J.-L.; Smith, J. American Institute of Physics (A.I.P.) Conference Proceedings: New York, 1991; pp. 131146.
76. Braun, W.; Go, N. J Mol Biol 1985, 186, 611.
77. Levitt, M. J Mol Biol 1983, 170, 723.
78. Beutler, T. C.; Mark, A. E.; van Schaik, R.; Gerber, P. R.; van Gunsteren, W. F Chem Phys Lett 1994, 222, 529.
79. Zacharias, M.; Straatsma, T. P.; McCammon, J. A. J Chem Phys 1994, 100, 9025.
80. Hornak, V.; Simmerling, C. J Mol Graph Modell 2004, 22,405.
81. Huber, T.; Torda, A. E.; van Gunsteren, W. F. J Phys Chem 1997, 101, 5926.
82. Piela, L.; Kostrowicki, J.; Scheraga, H. A. J Phys Chem 1989, 93, 3339.
83. Tsujishita, H.; Moriguchi, I.; Hirono, S. J Phys Chem 1993, 97, 4416.
84. Wenzel, W.; Hamacher, K. Phys Rev Lett 1999, 82, 3003.
85. Baumketner, A.; Shimizu, H.; Isobe, M.; Hiwatari, Y. Physica A 2002, 310, 139.
86. Pak, Y.; Wang, S. J Chem Phys 1999, 111, 4359.
87. Fukuda, I. Phys Rev E 2001, 64, Art. No. 016203.
88. Glover, F. ORSA J Computing 1989, 1, 190.
89. Glover, F. ORSA J Computing 1990, 2, 4.
90. Crippen, G. M.; Scheraga, H. A. Proc Natl Acad Sci USA 1969, 64, 42.
91. Huber, T.; Torda, A. E.; van Gunsteren, W. F. J Comp-Aided Mol Design 1994,8,695.
92. Laio, A.; Parrinello, M. Proc Natl Acad Sci U.S.A. 2002, 99, 12562.
93. Grubmüller, H. Phys Rev E 1995, 52, 2893.
94. Rahman, J. A.; Tully, J. C. Chem Phys 2002, 285, 277.
95. Hamelberg, D.; Mongan, J,; McCammon, J. A. J Chem Phys 2004, 120, 11919.
96. Torda, A. E.; Scheek, R. M.; van Gunsteren, W. F. J. Mol Biol 1990, 214, 223.
97. van Gunsteren, W. F. et al., In Methods in Enzymology: Nuclear Magnetic Resonance, Vol. 239; James, T. L.; Oppenheimer, N. J., Eds.; Academic Press: New York, USA, 1994; pp. 619-654.
98. Crippen, G. M. J Comput Chem 1982, 3, 471.
99. Purisima, E. O.; Scheraga. H. A. Proc Natl Acad Sci USA 1986, 83, 2782.
100. Crippen, G. M. J Phys Chem 1987, 91, 6341.
101. Crippen, G. M.; Havel, T. F. J Chem Inf Comp Sci 1990, 30, 220.
102. Weber, P. L.; Morrison, R.; Hare, D. L.; J Mol Biol 1988, 204, 483.
103. van Schaik, R. C.; Berendsen, H. J. C.; Torda, A. E.; van Gunsteren, W. F. J Mol Biol 1993, 234, 751.
104. Beutler, T. C.; van Gunsteren, W. F. J Chem Phys 1994, 101, 1417.
105. van Gunsteren, W. F.; Berendsen, H. J. C. Mol Phys 1977, 34, 1311.
106. Berendsen, H. J. C.; van Gunsteren, W. F. In Molecular-Dynamics Simulation of Statistical-Mechanical Systems, Proceedings of the International School of Physics "Enrico Fermi", Course 97; Ciccotti, G.; Hoover, W. G., Ed.; North-Holland: Amsterdam, 1986; pp. 43-65.
107. Marrink. S. J.; de Vries, A. H.; Mark, A. E. J Phys Chem B 2004, 108, 750.
108. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671.
109. Frantz, D. D.; Freeman, D. L.; Doll, J. D. J Chem Phys 1990, 93, 2769.
110. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola. A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
111. Mao, B.; Friedmann, A. R. Biophys J 1990, 58, 803.
112. Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. J Comput Chem 1999, 20, 786.
113. Gee, P. J.; van Gunsteren, W. F. Chem Eur J 2006, 12, 72.
114. VandeVondele, J.; Röthlisberger, U. J Phys Chem B 2002, 106, 203.
115. Elber. R.; Karplus, M. J Am Chem Soc 1990, 112, 9161.
116. Straub, J. E.; Karplus, M. J Chem Phys 1991, 94, 6737.
117. Zheng, Q. A.; Rusenfeld, R.; Vajda, S,; DeLisi, C. Prot Sci 1993, 2, 1242.
118. Olszewski, K. A.; Piela, L.; Scheraga, H. A. J Phys Chem 1992, 96, 4672.
119. Simmerling, C.; Miller, J. L.; Kollman, P. A. J Am Chem Soc 1998, 120,7149.
120. Liu, H. Y.; Duan, Z. H.; Luo, Q. M.; Shi, Y. Y. Prot Struct Func Gen 1999, 36, 462.
121. Goldberg, D. E. Genetic Algorithms in Search, Optimisation and Machine Learning; Addison-Wesley: Reading, 1989.
122. Sugita, Y.; Okamoto, Y. Chem Phys Lett 1999, 314, 141.
123. Okamoto, Y. J Mol Graph Modell 2004, 22, 425.
124. Zhou, R. H.; Berne, B. J.; Germain, R. Proc Natl Acad Sci U.S.A. 2001, 98, 14931.
125. Mitsutake, A.; Sugita, Y.; Okamoto, Y Biopolymers (Peptide Science) 2001, 60, 96.
126. Cheng, X. L.; Cui, G. L.; Hornak, V.; Simmerling, C. J Phys Chem B 2005, 109, 8220.
127. Voter, A. F. Phys Rev B 1998, 57, 13985.
128. Calvo, F.; Doye, J. P. K. Phys Rev E 2001, 63, Art. No. 010902.
129. Trebst, S.; Huse, D. A.; Troyer, M. Phys Rev E 2004, 70, Art. No. 046701.
130. Trebst, S.; Gull, E.; Troyer, M. J Chem Phys 2005, 123, Art. No. 204501.
131. Huber, T.; van Gunsteren, W. F. J Phys Chem A 1998, 102, 5937.
132. Hixson, C. A.; Wheeler, R. A. Phys Rev E 2001, 64, Art. No. 026701.
133. Huber, G. A.; McCammon, J. A. Phys Rev E 1997, 55, 4822.
134. Shirts, M. R.; Pande, V. S. Phys Rev Lett 2001, 86, 4983.
135. Dauber, P.; Maunder, C. M.; Osguthorpe, D. J. J Comput-Aided Mol Des 1996, 10, 177.
136. Phillips, S. C.; Essex, J. W.; Edge, C. M. J Chem Phys 2000, 112, 2586.
137. Phillips, S. C.; Swain, M. T.; Wiley, A. P.; Essex, J. W.; Edge, C. M. J Phys Chem B 2003, 107, 2098.
138. Amadei, A.; Linssen, A. B. M.; de Groot, B. L.; van Aalten, D. M. F.; Berendsen, H. J. C. J Biomol Struct Dyn 1996, 13, 615.
139. Abseher, R.; Nilges, M. Proteins: Struct, Funct, Bioinf 2000, 39, 82.
140. Kleinjung, J.; Fraternali, F.; Martin, S. R.; Bayley, P. M. Proteins 2003, 50, 648.
141. Zhang, Z.; Shi, Y.; Liu, H. Biophys J 2003, 84, 3583.
142. Christen, M.; Kunz, A.-P. E.; van Gunsteren, W. F. J Chem Phys 2006, 110, 84.
143. Torrie, G. M.; Valleau, J. P. J Comput Phys 1977, 23, 187.
144. Schlitter, J.; Engels, M.; Kruger, P. J Mol Graph 1994, 12, 84.
145. Mulders, T.; Kruger, P.; Swegat, W.; Schlitter, J. J Chem Phys 1996, 104, 4869.
146. Coluzza, I.; Sprik, M.; Ciccotti, G. Mol Phys 2003, 101, 2885.
147. Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. J Chem Phys 1998, 108, 1964.
148. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu Rev Phys Chem 2002, 53, 291.
149. Dellago, C.; Bolhuis, P. G.; Geissler, P. L. Adv Chem Phys 2003,123,1.
150. Moroni, D.; van Erp, T. S.; Bolhuis, P. G. Physica A 2004, 340, 395.
151. Weinan, E.; Ren, W. Q.; Vanden-Eijnden, E. Phys Rev B 2002, 66, 052301.
152. Weinan, E.; Ren, W. Q.; Vanden-Eijnden, E. J Phys Chem B 2005,109, 6688.
153. Jonsson, H,; Mills, G.; Jacobsen, K. W. In Classical and Quantum Dynamics in Condensed Phase Simulations; Berne, B. J.; Ciccotti, G.; Coker, D. F., Ed.; World Scientific: Singapore, 1998.
154. Chu, J. W.; Trout, B. L.; Brooks, B. R. J Chem Phys 2003, 119, 12708.
155. Crehuet, R.; Field, M. J. J Chem Phys 2003, 118, 9563.
156. Xie, L.; Liu, H.; Yang, W. J Chem Phys 2004, 120, 8039.
157. Voter, A. F. J Chem Phys 1997, 106, 4665.
158. Voter, A. F. Phys Rev Lett 1997, 78, 3908.
159. Hummer, G.; Kevrekidis, I. G. J Chem Phys 2003, 18, 10762.
160. Koehl, P.; Delarue, M. J Mol Biol 1994, 239, 249.
161. Huber, T.; Torda, A. E.; van Gunsteren, W. F. Biopolymers 1996, 39, 103.
162. van Gunsteren, W. F.; Daura, X.; Mark, A. E. Helv Chim Acta 2002, 85, 3113.
163. Berne, B. J.; Straub, J. E. Curr Op Struct Biol 1997, 7, 181.
164. Tai, K. Biophys Chem 2004, 107, 213.
165. Voter, A. F.; Montalenti, F.; Germann, T. C. Annu Rev Mater Res 2002, 32, 321.