Observations on the A versus B Equilibrium in Molecular Dynamics Simulations of Duplex DNA and RNA

ACS Symposium Series

Volumn 682, Issue , 1998, Pages 304-311

  MacKerell Jr , Alexander D ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF PHARMACY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0345983594     PISSN: 00976156     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (29)

1. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins, A Theoretical Perspective Dynamics, Structure, and Thermodynamics; John Wiley and Sons: New York, 1988; Vol. LXXI.
2. McCammon, J. A.; Harvey, S. Dynamics of Proteins and Nucleic Acids; Cambridge University Press;, 1987.
3. Pastor, R. W. Curr. Opin. Struct. Biol. 1994, 4, 486-492.
4. Tobias, D. J.; Tu, K.; Klein, M. L. Curr. Opin. Coll. & Inter. Sci. 1997, 2, 15-26.
5. Norberg, J.; Nilsson, L. J. Chem. Phys. 1996, 104, 6052-6057.
6. Cheatham, T. E., III; Kollman, P. A. J. Mol. Biol. 1996, In Press.
7. Yang, L.; Pettitt, B. M. J. Phys. Chem. 1996, 100, 2550-2566.
8. Young, M. A.; Jayaram, B.; Beveridge, D. L. J. Am. Chem. Soc. 1997, 119, 59-69.
9. MacKerell, A. D., Jr. J. Phys. Chem. B 1997, 101, 646-650.
10. Auffinger, P.; Westhof, E. Encyc. Comp. Chem. 1997, In press.
11. MacKerell, A. D., Jr.; Wiórkiewicz-Kuczera, J.; Karplus, M. J. Am. Chem. Soc. 1995, 117, 11946-11975.
12. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, J., K.M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Amer. Chem. Soc. 1995, 117, 5179-5197.
13. Lee, H.; Darden, T.; Pedersen, L. G. J. Chem. Phys. 1995, 102, 3830-3834.
14. York, D. M.; Yang, W.; Lee, H.; Darden, T.; Pedersen, L. G. J. Am. Chem. Soc. 1995, 117, 5001-5002.
15. Cheatham, T. E., III; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. J. Am. Chem, Soc. 1995, 117, 4193-4194.
16. Weerasinghe, S.; Smith, P. E.; Mohan, V.; Cheng, Y.-K.; Pettitt, B. M. J. Am. Chem. Soc. 1995, 117, 2147-2158.
17. Ewald, P. P. Ann. Phys. 1921, 64, 253-287.
18. Darden, T. A.; York, D.; Pedersen, L. G. J. Chem. Phys. 1993, 98, 10089-10092.
19. Norberg, J.; Nilsson, L. J. Biomol. NMR 1996, 7, 305-314.
20. Cheatham, I., T.E.; Kollman, P. A. J. Amer. Chem. Soc. 1997, 119, 4805-4825.
21. Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S.-H.; Srinivasan, A. R.; Schneider, B. Biophys. J. 1992, 63, 751-759.
22. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
23. Arnott, S.; Hukins, D. W. L. J. Mol. Biol. 1973, 81, 93-105.
24. Jorgensen, W. L. J. Am. Chem. Soc. 1981, 103, 335.
25. Reiher, W. E., III. Theoretical Studies of Hydrogen Bonding. Ph.D., Harvard University, 1985.
26. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comp. Phys. 1977, 23, 327-341.
27. Ravishanker, G.; Swaminathan, S.; Beveridge, D. L.; Lavery, R.; Sklenar, H. J. Biomol. Str. Dyn. 1989, 6, 669-699.
28. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
29. Cheatham, I., T.E.; Kollman, P. A. Structure 1997, In Press.