Automatic method for identifying reaction coordinates in complex systems

Journal of Physical Chemistry B

Volumn 109, Issue 14, 2005, Pages 6769-6779

  Ma, Ao ^a   Dinner, Aaron R ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REACTION DYNAMICS; SOLVENT-DERIEVED ELECTROSTATIC TORQUE; TRANSITION PATH SAMPLING; TRANSITION STATES; WATER MOLECULES;

COMPUTER SIMULATION; DATABASE SYSTEMS; GENETIC ALGORITHMS; ISOMERIZATION; LARGE SCALE SYSTEMS; POLYPEPTIDES; SOLVENTS; WATER;

CHEMICAL REACTIONS;

ALANINE; CARBON; DIPEPTIDE; SOLVENT;

ARTICLE; ARTIFICIAL NEURAL NETWORK; AUTOMATION; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ELECTRICITY; STATIC ELECTRICITY; SYSTEMS BIOLOGY; THEORETICAL MODEL; THERMODYNAMICS;

ALANINE; AUTOMATION; CARBON; COMPUTER SIMULATION; DIPEPTIDES; ELECTROSTATICS; MODELS, CHEMICAL; MODELS, GENETIC; MODELS, MOLECULAR; MODELS, THEORETICAL; MOLECULAR CONFORMATION; NEURAL NETWORKS (COMPUTER); SOLVENTS; STATIC ELECTRICITY; SYSTEMS BIOLOGY; THERMODYNAMICS;

EID: 17544374740     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp045546c     Document Type: Article

References (51)

1. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, 1987.
2. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu. Rev. Phys. Chem. 2002, 53, 291.
3. Dellago, C.; Bolhuis, P. G.; Geissler, P. L. Adv. Chem. Phys. 2002, 123, 1.
4. Elber, R.; Ghosh, A.; Cardenas, A.; Stern, H. Adv. Chem. Phys. 2003, 126, 93.
5. E, W.; Ren, W.; Vanden-Eijnden, E. J. Appl. Phys. 2003, 93, 2275.
6. Zukerman, D. M.; Woolf, T. B. Phys. Rev. E 2000, 63, 016702.
7. Dinner, A. R.; Karplus, M. J. Phys. Chem. B 1999, 103, 7976.
8. Dinner, A. R.; Sali, A.; Smith, L. J.; Dobson, C. M.; Karplus, M. Trends Biochem. Sci. 2000, 25, 331.
9. McCormick, T. A.; Chandler, D. J. Phys. Chem. B 2003, 107, 2796.
10. Valleau, J. P.; Card, D. N. J. Chem. Phys. 1972, 57, 5457.
11. Tome, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187.
12. Chandler, D. J. Chem. Phys. 1978, 68, 2959.
13. Komatsuzaki, T.; Berry, R. S. Adv. Chem. Phys. 2002, 123, 79.
14. Karplus, M.; Porter, R. N.; Shanna, R. D. J. Chem. Phys. 1965, 43, 3259.
15. Karplus, M.; Sharma, R. D.; Porter, R. N. J. Chem. Phys. 1964, 40, 2033.
16. Geissler, P. L.; Dellago, C.; Chandler, D. J. Phys. Chem. B 1999, 103, 3706.
17. Bolhuis, P. G.; Dellago, C.; Chandler, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5877.
18. Hagan, M. F.; Dinner, A. R.; Chandler, D.; Chakraborty, A. K. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13922.
19. Becker, O. M.; Karplus, M. J. Chem. Phys. 1997, 106, 1495.
20. Elmaci, N.; Berry, R. S. J. Chem. Phys. 1999, 110, 10606.
21. Doruker, P.; Atilgan, A. R.; Bahar, I. Proteins 2000, 40, 512.
22. Schmidt, M.; Rajagopal, S.; Ren, Z.; Moffat, K. Biophys. J. 2002, 84, 2112.
23. Du, R.; Pande, V. S.; Grosberg, A. Y.; Tanaka, T.; Shakhnovich, E. S. J. Chem. Phys. 1998, 108, 334.
24. Northrup, S. H.; Pear, M. R.; Lee, C.-Y.; McCammon, J. A.; Kaiplus, M. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 4035.
25. So, S.-S.; Karplus, M. J. Med. Chem. 1996, 39, 1521.
26. So, S.-S.; Karplus, M. J. Med. Chem. 1996, 39, 5246.
27. Dinner, A. R.; So, S.-S.; Karplus, M. Proteins 1998, 33, 177.
28. Dinner, A. R.; Karplus, M. Nat. Struct. Biol. 2001, 8, 21.
29. Dinner, A. R.; So, S.-S.; Karplus, M. Adv. Chem. Phys. 2002, 120, 1.
30. ten Wolde, P. R.; Chandler, D. Proc. Natl Acad. Sci. U.S.A. 2002, 99, 6539.
31. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathm, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
32. Dinner, A. R. Monte Carlo Simulations of Protein Folding. Thesis, Harvard University, 1999.
33. Neria, E.; Fischer S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902.
34. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; Debolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1.
35. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
36. Schaefer, M.; Karplus, M. J. Phys. Chem. 1996, 100, 1578.
37. Schaefer, M.; Bartels, C.; Leclerc, F.; Karplus, M. J. Comput. Chem. 2001, 22, 1857.
38. Calimet, N.; Schaefer, M.; Simonson, T. Proteins 2001, 45, 144.
39. Schaefer, M.; Karplus, M. J. Mol. Biol. 1998, 284, 835.
40. Smith, P.; Pettitt, B. M. J. Phys. Chem. 1993, 97, 6907.
41. Singhal, N.; Snow, C. D.; Pande, V. S. J. Chem. Phys. 2004, 121, 415.
42. Rossky, P. J.; Simon, J. D. Science 1994, 370, 263.
43. Neumann, M. J. Chem. Phys. 1985, 82, 5663.
44. Kurtović, Z.; Marchi, M.; Chandler, D. Mol. Phys. 1993, 78, 1155.
45. Geissler, P. L.; Dellago, C.; Chandler, D.; Hutter, J.; Parrinello, M. Science 2001, 291, 2121.
46. Chandler, D. Nature 2002, 417, 491.
47. Rhee, Y. M.; Sorin, E. J.; Jayachandran, G.; Lindahl, E.; Pande, V. S. Proc. Natl. Acad. Sci. U.SA. 2004, 101, 6456.
48. Truhlar, D. G.; Garrett, B. C. J. Phys. Chem. B 2000, 104, 1069.
49. Grote, R. F.; Hynes, J. T. J. Chem. Phys. 1980, 73, 2715.
50. van der Zwan, G.; Hynes, J. T. J. Chem. Phys. 1983, 78, 4174.
51. van der Zwan, G.; Hynes, J. T. Chem. Phys. 1984, 90, 21.