Molecular dynamics simulations of the d(CCAACGTTGG) 2 decamer in crystal environment: Comparison of atomic point-charge, extra-point, and polarizable force fields

Journal of Chemical Physics

Volumn 121, Issue 14, 2004, Pages 6998-7008

  Baucom, Jason ^a   Transue, Thomas ^b   Fuentes Cabrera, Miguel ^a   Krahn, J M ^b   Darden, Thomas A ^b   Sagul, Celeste ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMIC POINT-CHARGES; EXTRA-POINTS; MULTIPOLAR COMPONENTS; POLARIZABLE FORCE FIELDS;

COMPUTER SIMULATION; CRYSTAL STRUCTURE; DNA; ELECTRIC CONTACTS; MOLECULAR CRYSTALS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; POLARIZATION; X RAY CRYSTALLOGRAPHY;

CRYSTAL ATOMIC STRUCTURE;

OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; CRYSTALLIZATION; DNA SEQUENCE; THERMODYNAMICS;

COMPUTER SIMULATION; CRYSTALLIZATION; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; SEQUENCE ANALYSIS, DNA; THERMODYNAMICS;

EID: 7544244858     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1788631     Document Type: Article

References (42)

1. D. M. York, T. A. Darden, and L. G. Pedersen, J. Chem. Phys. 99. 8345 (1993).
2. D. M. York et al., J. Am. Chem. Soc. 117. 5001 (1995).
3. P. J. Steinbach and B. R. Brooks, J. Comput. Chem. 15, 667 (1994).
4. T. A. Darden, D. M. York, and L. G. Pedersen, J. Chem. Phys. 98. 10089 (1993).
5. U. Essmann et al., J. Chem. Phys. 103, 8577 (1995).
6. D. Beveridge and K. McConnell, Curr. Opin. Struct. Biol. 10, 182 (2000).
7. J. Norberg and L. Nilsson, Acc. Chem. Res. 35, 465 (2002).
8. T. E. Cheatham III and M. Young, Biopolymers 56, 232 (2000).
9. C. Sagui and T. A. Darden, Annu. Rev. Biophys. Biomol. Struct 28, 155 (1999).
10. T. E. Cheatham III and P. A. Kollman, Annu. Rev. Phys. Chem. 51, 435471 (2000).
11. H. Lee, T. A. Darden, and L. G. Pedersen, J. Chem. Phys. 102. 3830 (1995).
12. H. Lee, T. A. Darden, and L. G. Pedersen, Chem. Phys. Lett. 243. 229 (1995).
13. A. MacKerell, J. Wiorkiewicz-Kuczera, and M. Karplus, J. Am. Chem. Soc. 117, 11946 (1995).
14. T. E. Cheatham III and P. A. Sollman, J. Mol. Biol. 259, 434 (1996).
15. G. Prive, K. Yanagi, and R. Dickerson, J. Mol. Biol. 217, 177 (1991).
16. D. Bevan, L. Li, L. Pedersen, and T. Darden, Biophys. J. 78, 668 (2000).
17. W. Cornell et al., J. Am. Chem. Soc. 117, 5179 (1995).
18. P. Ren and J. W. Ponder, J. Comput. Chem. 23, 1497 (2002).
19. C. Sagui, P. Pomorski, T. A. Darden. and C. Roland. J. Chem. Phys. 120. 4530 (2004).
20. C. Sagui, L. Pedersen, and T. A. Darden, J. Chem. Phys. 120, 73 (2004).
21. L. McMurchie and E. Davidson, J. Comput. Phys. 26, 218 (1978).
22. C. Sagui and T. A. Darden, J. Chem. Phys. 114, 6578 (2001).
23. A. Toukmaji, C. Sagui, J. A. Board, and T. Darden, J. Chem. Phys. 113. 10913 (2000).
24. W. Smith, CCP5 Information Quarterly 4, 13 (1982).
25. D. A. Case et al., computer code AMBER 7, University of California, San Francisco, 2002.
26. D. A. Pearlman et al., Comput Phys. Commun. 91, l (1995).
27. P. Ren and J. W. Ponder, J. Phys. Chem. B 107, 5933 (2003).
28. J. W. Ponder and D. A. Case. Adv. Protein Chem. 66, 27 (2003).
29. T. E Cheatham III, P. Cieplak, and P. A. Kollman, J. Biomol. Struct. Dyn. 16, 845 (1999).
30. R. Dixon and P. Kollman, J. Comput Chem. 18, 1632 (1997).
31. W. Jorgensen, J. Chandrasekhar, J. Madura, and M. Klein, J. Chem. Phys. 79, 926 (1983).
32. J. Caldwell and P. Kollman, J. Phys. Chem. 99, 6208 (1995).
33. M. Mahoney and W. Jorgensen, J. Chem. Phys. 112, 8910 (2000).
34. X. Lu, Z. Shakked, and W. Olson, J. Mol. Biol. 300, 819 (2000).
35. X. Lu and W. Olson, Nucleic Acids Res. 31, 5108 (2003).
36. P. Várnai, D. Djuranovic, R. Lavery, and B. Hartmann, Nucleic Acids Res. 30. 5398 (2002).
37. R. Lavery, in Advances in Computational Biology, Vol. 1, p. 69, edited by H. O. Villar (Jai Press, 1994).
38. T. E. Chearham III and P. A. Kollman, J. Am. Chem. Soc. 119, 4805 (1997).
39. P. Cieplak, T. E. Cheatham III, and P. A. Kollman, J. Am. Chem. Soc. 119, 6722 (1997).
40. M. A. El Hassan and C. R. Calladine, J. Mol. Biol. 282. 331 (1998).
41. R. Dickerson, D. Goodsell, and S. Neidle. Proc. Natl. Acad. Sci. U.S.A. 91, 3579 (1994).
42. X. Xu, W. Chiu, and S. Au-Yeung, J. Am. Chem. Soc. 120, 4230 (1994).