Principal component analysis and long time protein dynamics

Journal of Physical Chemistry

Volumn 100, Issue 7, 1996, Pages 2567-2572

  Balsera, M A ^a   Wriggers, W ^a   Oono, Y ^a   Schulten, K ^a  

^a United States of America   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001295503     PISSN: 00223654     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9536920     Document Type: Article

References (35)

1. Karplus, M. Molecular Dynamics: Applications to Proteins. In Rivail, J.-L., Ed.; Modelling of Molecular Structures and Properties, volume 71 of Studies in Physical and Theoretical Chemistry; Elsevier Science Publishers: Amsterdam, 1990; pp 427-461.
2. Brooks, C. L.; et al. Proteins; Wiley-Interscience: New York 1988; Chapter 2.B, pp 14-21.
3. yan Chang, X.; Freed, K. F. J. Chem. Phys. 1993, 99 (10), 8016-8030.
4. Nyberg, A.; Schlick, T. Chem. Phys. Lett. 1992, 198, 538.
5. Karhunen, K. Ann. Acad. Sci. Fenn. 1947, 37.
6. Brooks, B. B.; et al. J. Comput. Chem. 1995, 16 (12), 1522-1542.
7. Case, D. A. Curr. Opin. Struct. Biol. 1994, 4, 285-290.
8. Karplus, M.; Jushick, J. N. Macromolecules 1981, 14, 325-332.
9. Perahia, D.; et al. Biopolymers 1990, 29, 645-677.
10. Ichiye, T.; Karplus, M. Proteins 1991, 11, 205-217.
11. Horiuchi, T.; Go, N. Proteins 1990, 10, 106-116.
12. Kitao, A.; et al. J. Chem. Phys. 1991, 158, 447-472.
13. Amadei, A.; et al. Proteins 1993, 17, 412-425.
14. van Aalten, D. M. F.; et al. Proteins 1995, 22, 45-54.
15. Garcia, A. E. Phys. Rev. Lett. 1992, 68, 2696-2699.
16. Sirovich, I.; Rodriguez, J. D. Phys. Lett. A 1987, 120, 211-214.
17. Nicholson, L. K.; et al. Struct. Biol. 1995, 2, 274-280.
18. Hodel, A.; et al. Protein Sci. 1995, 4, 636-654.
19. Clarage, J. B.; et al. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 3288-3292.
20. Faure, P.; et al. Struct. Biol. 1994, 1 (2), 124-128.
21. Bruschweiler, R.; Case, D. A. Phys. Rev. Lett. 1994, 72, 940-943.
22. Peyret, R.; Taylor, T. D. Computational Methods for Fluid Flow; Springer Verlag: Berlin, 1983.
23. Doi, M.; Edwards, S. F. The Theory of Polymer Dynamics; Oxford Science Publications: Oxford, 1986.
24. Devreotes, P. N.; Zigmond, S. H. Ann. Rev. Cell Biol. 1988, 4, 649-686.
25. Small, J. V. Curr. Opin. Cell Biol. 1989, 1, 75-79.
26. Theriot, J. A.; et al. Nature 1992, 357, 257-260.
27. Holmes, K. C.; et al. Nature 1990, 347, 44-49.
28. Lorenz, M.; et al. J. Mol. Biol. 1993, 234, 826-836.
29. Kabsch, W.; et al. Nature 1990, 347, 37-44.
30. Tirion, M. M.; ben-Avraham, D. J. Mol. Biol. 1993, 230, 186-195.
31. Tirion, M. M.; et al. Biophys. J. 1995, 68, 5-12.
32. Brünger, A. T. X-PLOR. Version 3.1, A System for X-ray Crystallography and NMR; The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, 1992.
33. Wriggers, W.; Schulten, K. Manuscript in preparation.
34. Brooks, B. B.; et al. J. Comput. Chem. 1995, 16 (12), 1554-1566.
35. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, 1987; Chapter 6.4.1.