Quantitative computer simulations of biomolecules: A snapshot

Journal of Computational Chemistry

Volumn 29, Issue 4, 2008, Pages 668-672

  Yang, Wei ^a   Nymeyer, Hugh ^a   Zhou, Huan Xiang ^a,b   Berg, Bernd ^a,b   Brüschweiler, Rafael ^a,c  

^a FLORIDA STATE UNIVERSITY   (United States)

^b Florida State University   (United States)

^c FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Enhanced sampling; Improved MD force fields; Protein protein interactions; Statistical convergence

Indexed keywords

COMPUTATIONAL BIOPHYSICS; ENHANCED SAMPLING; PROTEIN-PROTEIN INTERACTIONS;

BIOPHYSICS; CHEMICAL ANALYSIS; COMPUTER SIMULATION; CONVERGENCE OF NUMERICAL METHODS; PROTEINS;

BIOMOLECULES;

PROTEIN;

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; METABOLISM; PROTEIN BINDING;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ELECTROSTATICS; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEINS;

EID: 39049086324     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20819     Document Type: Article

References (70)

1. Buck, M.; Bouguet-Bonnet, S.; Pastor, R. W.; MacKerell, A. D. Jr. Biophys J 2006, 90, L36.
2. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins Struc Func Inf 2006, 65, 712.
3. Mackerell, A. D. Jr. J Comp Chem 2004, 25, 1584.
4. Lipari, G.; Szabo, A. J Am Chem Soc 1982, 104, 4546.
5. Case, D. A. Ace Chem Res 2002, 35, 325.
6. Showalter, S. A.; Brüschweiler, R. J Chem Theor Comp 2007, 3, 961.
7. Hamelberg, D.; Mongan, J.; McCammon, J. A. J Chem Phys 2004, 120, 11919.
8. Markwick, P.; Bouvignies, G.; Blackledge, M. J Am Chem Soc 2007, 129, 4724.
9. Bax, A.; Grishaev, A. Curr Opin Struc Biol 2005, 15, 563.
10. Showalter, S. A.; Brüschweiler, R. J Am Chem Soc 2007, 129, 4158.
11. Patel, S.; Brooks, C. L., III. Mol Sim 2006, 32, 231.
12. Lamoureux, G.; MacKerell, A. D.; Roux, B. J Chem Phys 2003, 119, 5185.
13. Patel, S.; Brooks, C. L., III. J Comp Chem 2004, 25, 1.
14. Patel, S.; Mackerell, A. D. Jr.; Brooks, C. L., III. J Comp Chem 2004, 25, 1504.
15. Vorobyov, I.; Anisimov, V. M.; Mackerell, A. D. Jr. J Phys Chem B 2005, 109, 18988.
16. Lopes, P. E. M.; Lamoureux, G.; Roux, B.; MacKerell, A. D. Jr. J Phys Chem B 2007, 111, 2873.
17. Vorobyov, I.; Anisimov, V. M.; Greene, S.; Venable, R. M.; Moser, A.; Richard, W.; MacKerell, A. D. Jr. J Chem Theor Comp 2007, 3, 1120.
18. Anisimov, V. M.; Lamoureux, G.; Vorobyov, I. V.; Huang, N.; Roux, B.; MacKerell, M. D. J Chem Theor Comp 2005, 1, 153.
19. Patel, S.; Brooks, C. L., III. J Chem Phys 2005, 122, 024508.
20. Patel, S.; Brooks, C. L., III. J Chem Phys 2005, 123, 164502.
21. Patel, S.; Brooks, C. L.. III. J Chem Phys 2005, 124, 204706.
22. Harder, E.; Anisimov, V. M.; Vorobyov, I. V.; Lopes, P. E. M.; Noskov, S. Y.; Sergei, Y.; MacKerell, A. D.; Roux, B. J Chem Theor Comp 2006, 2, 1587.
23. Repasky, M. P.; Chandrasekhar, J.; Jorgensen, W. L. J Comp Chem 2002, 23, 1601.
24. Tubert-Brohman, I.; Guimaraes, C. R. W.; Jorgensen, W. L. J Chem Theor Comp 2005, 1, 817.
25. Tubert-Brohman, I.; Guimaraes, C. R. W.; Repasky, M. P.; Jorgensen, W. L. J Comp Chem 2004, 25, 138.
26. Sattelmeyer, K. W.; Tirado-Rives, J.; Jorgensen, W. L. J Phys Chem A 2006, 110, 13551.
27. Acevedo, O.; Jorgensen, W. L. J Am Chem Soc 2005, 127, 8829.
28. Acevedo, O.; Jorgensen, W. L. J Am Chem Soc 2006, 128, 6141.
29. Tubert-Brohman, I.; Acevedo, O.; Jorgensen, W. L. J Am Chem Soc 2006, 128, 16904.
30. Nam, K.; Cui, Q.; Gao, J. L.; York, D. M. J Chem Theor Comp 2007, 3, 486.
31. Schaefer, P.; Riccardi, D.; Cui, Q. J Chem Phys 2005, 123, 014905.
32. Wang, B.; Brothers, E. N.; van der Vaart, A. J Chem Phys 2004, 120, 11392.
33. Wang, B.; Raha, K.; Merz, K. M. J Am Chem Soc 2004, 126, 11430.
34. Wang, B.; Merz, K. M. J Am Chem Soc 2005, 127, 5310.
35. Wang, B.; Merz, K. M. J Chem Theor Comp 2006, 2, 209.
36. Alsallaq, R.; Zhou, H.-X. Structure 2007, 15, 215.
37. Gilson, M. K.; Zhou, H.-X. Annu Rev Biophys Biomol Struct 2007, 36, 21.
38. Dong, F.; Vijayakumar, M.; Zhou, H.-X. Biophys J 2003, 85, 49.
39. Dong, F.; Zhou, H.-X. Proteins Struc Func Bioinf 2006, 65, 87.
40. Zhang, L.; Mallik, B.; Morikis, D. J Mol Biol 2007, 369, 567.
41. Qin, S.; Zhou, H. X. Biopolymers 2007, 86, 112.
42. Zhou, H.-X. J Chem Phys 1996, 105, 7235.
43. Huang, X.; Dong, F.; Zhou, H.-X. J Am Chem Soc 2005, 127, 6836.
44. Wang, J.; Zhang, K.; Lu, H.; Wang, E. Biophys J 2006, 91, 866.
45. Wang, J.; Xu, L.; Wang, E. Biophys J 2007, 92, L109.
46. Torrie, G. M.; Valleau, J. P. J Comp Phys 1977, 23, 187.
47. Berg, B.; Neuhaus, T. Phys Rev Lett 1992, 68, 9.
48. Swendsen, R. H.; Wang, J.-S. Phys Rev Lett 1986, 57, 2607.
49. Nadler, W.; Hansmann, U. H. E. Phys Rev E 2007, 75 026109.
50. Berg, B.; Muguruma, C.; Okamoto, Y. Phys Rev B 2007, 75, 092202.
51. Khandogin, J.; Brooks, C. L., III. Biochemistry 2006, 45, 9363.
52. Lyman, E.; Ytreberg, F. M.; Zuckerman, D. M. Phys Rev Lett 2006, 96, 028105.
53. Li, H.; Li, G.; Berg, B. A.; Yang, W. J Chem Phys 2006, 125, 144902.
54. Okur, A.; Roe, D. R.; Cui, G. L.; Hornak, V.; Simmerling, C. J Chem Theor Comp 2007, 3, 557.
55. Roitberg, A. E.; Okur, A.; Simmerling, C. J Phys Chem B 2007, 111, 2415.
56. Trebst, S.; Troyer, M.; Hansmann, U. H. E. J Chem Phys 2006, 124, 174903.
57. Li, H.; Yang, W. J Chem Phys 2007, 126, 114104.
58. Kwak, W.; Hansmann, U. H. E. Phys Rev Lett 2005, 95, 138102.
59. Li, H.; Fajer, M.; Yang, W. J Chem Phys 2007, 126, 24106.
60. Min, D.; Li, H.; Li, G.; Bitetti-Putzer, R.; Yang, W. J Chem Phys 2007, 126, 144109.
61. Itoh, S. G.; Okamoto, Y. J Chem Phys 2006, 124, 104103.
62. Neuhaus, T.; Hager, J. Phys Rev E 2006, 74, 036702.
63. Min, D.; Liu, Y.; Carbone, I.; Yang, W. J Chem Phys 2007, 126, 194104.
64. Li, H.; Min, D.; Liu, Y.; Yang, W. J Chem Phys 2007, in press.
65. Xing, C.; Andricioaei, I. J Chem Phys 2006, 124, 34110.
66. Sokal, A. D. Cours de Troisieme Cycle de la Physique en Suisse Romande; Lausanne: Switzerland, 1996.
67. Berg, B. A. Markov Chain Monte Carlo Simulations and Their Statistical Analysis With Web-Based Fortran Code; World Scientific: Hackensack, NJ, 2004.
68. Flyvbjerg, H.; Petersen, H. G. J Chem Phys 1989, 91, 461.
69. Paschek, D.; Nymeyer, H.; Garcia, A. E. J Struct Biol 2007, 157, 524.
70. van der Spoel, D.; Seibert, M. M. Phys Rev Lett 2006, 96, 238102.