A modified version of the cornell et al. force field with improved sugar pucker phases and helical repeat

Journal of Biomolecular Structure and Dynamics

Volumn 16, Issue 4, 1999, Pages 845-862

  Cheatham, Thomas E ^a   Cieplak, Piotr ^b   Kollman, Peter A ^c  

^a NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^b UNIVERSITY OF WARSAW   (Poland)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEIC ACID;

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; DNA HELIX; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; NUCLEIC ACID ANALYSIS; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL;

COMPUTER SIMULATION; DNA; ELECTROSTATICS; KINETICS; MODELS, STATISTICAL; RNA, DOUBLE-STRANDED; SEQUENCE ANALYSIS, DNA; SUGAR PHOSPHATES; TIME FACTORS;

EID: 0032922174     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1999.10508297     Document Type: Article

References (79)

1. Cheatham, T. E., III and Kollman, P. A., 1996. J. Mol. Biol., 259:434–444.
2. Cheatham, T. E., III and Kollman, P. A., 1997. J. Amer. Chem. Soc., 119:4805–4825.
3. Duan, Y., Wilkosz, P., Crowley, M., and Rosenberg, J. M., 1997. J. Mol. Biol., 272:553–572.
4. Feig, M., and Pettitt, B. M., 1997. J. Phys. Chem., 101:7361–7363.
5. Young, M. A., Ravishanker, G., and Beveridge, D. L., 1997. Biophys. J., 73:2313–2336.
6. Feig, M., and Pettitt, B. M., 1998. Biophys. J., 75:134–149.
7. Flatters, D., and Lavery, R., 1998. Biophys. J., 75:372–381.
8. Young, M. A., and Beveridge, D. L., 1998. J. Mot. Biol., 281:675–687.
9. Cheatham, T. E., III, Crowley, M. F., Fox, T., and Kollman, P. A., 1997. Proc. Natl. Acad. Sci., 94:9626–9630.
10. Cheatham, T. E., III and Kollman, P. A., 1997. Structure, 5:1297–1311.
11. Langley, D. R., 1998. J. Biomol. Struct. Dyn., [in press]
12. MacKerell, A. D., Jr. 1997. J. Phys. Chem., B101:646–650.
13. Sprous, D., Young, M. A., and Beveridge, D. L., 1998. J. Phys. Chem. B., 102:4658–4667.
14. Young, M. A., Jayaram, B., and Beveridge, D. L., 1997. J. Amer. Chem. Soc., 119:59–69.
15. Miaskiewicz, K., Miller, J., Cooney, M., and Osman, R., 1996. J. Amer. Chem. Soc., 118:9156–9163.
16. Spector, T. I., Cheatham, T. E., III and Kollman, P. A., 1997. J. Amer. Chem. Soc., 119:7095–7104.
17. Cieplak, P., Cheatham, T. E., III and Kollman, P. A., 1997. J. Amer. Chem. Soc., 119:6722–6730.
18. Luo, J., and Bruice, T. C., 1997. J. Amer. Chem. Soc., 119:6693–6701.
19. Luo, J., and Bruice, T. C., 1998. J. Amer. Chem. Soc., 120:1115–1123.
20. Sen, S., and Nilsson, L., 1998. J. Amer. Chem. Soc., 120:619–631.
21. Shields, G. C., Laughton, C. A., and Orozco, M., 1998. J. Amer. Chem. Soc., 120:5895–5904.
22. Bostock-Smith, C. E., Laughton, C. A., and Searle, M. S., 1998. Nue. Acids Res., 26:1660–1667.
23. Zichi, D. A., 1995. J. Amer. Chem. Soc., 117:2957–2969.
24. Miller, J. L., and Kollman, P. A., 1997. J. Mol. Biol., 270:436–450.
25. Miller, J. L., and Kollman, P. A., 1997. Biophys. J., 73:2702–2710.
26. Auffinger, P., and Westhof, E., 1996. Biophys. J., 71:940–954.
27. Auffinger, P., Louise-May, S., and Westhof, E., 1996. J. Amer. Chem. Soc., 118:1181–1189.
28. Auffinger, P., and Westhof, E., 1997. J. Mol. Biol., 269:326–341.
29. Hermann, T., Auffinger, P., Scott, W. G., and Westhof, E., 1997. Nue. Acids Res., 25:3421–3427.
30. Hermann, T., Auffinger, P., and Westhof, E., 1998. Eur. Biopys. J., 27:153–165.
31. Weerasinghe, S., Smith, P. E., Mohan, V., Cheng, Y. K., and Pettitt, B. M., 1995. J. Amer. Chem. Soc., 117:2147–2158.
32. Weerasinghe, S., Smith, P. E., and Pettitt, B. M., 1995. Biochem., 34:16269–16278.
33. Shields, G. C., Laughton, C. A., and Orozco, M., 1997. J. Amer. Chem. Soc., 119:7463–7469.
34. Spackova, N., Berger, I., Egli, M., and Sponer, J., 1998. J. Amer. Chem. Soc., 120:6147–6151.
35. Strahan, G. D., Keniry, M. A., and Shafer, R. H., 1998. Biophys. J., 75:968–981.
36. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G., 1995. J. Chem. Phys., 103:8577–8593.
37. Pearl man, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Debolt, S., Ferguson, D., Seibel, G., and Kollman, P., 1995. Comp. Phys. Comm., 91:1–41.
38. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., 1995. J. Amer. Chem. Soc., 117:5179–5197.
39. Saenger, W., 1984. Principles of Nucleic Acid Structure New York:Springer-Verlag.
40. Peck, L. J., and Wang, J. C., 1981. Nature, 292:375–378.
41. Rhodes, D., and Klug, A., 1980. Nature, 286:573–578.
42. Ulyanov, N. B., and James, T. L., 1995. Meth. Enzym., 261:90–120.
43. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D., Swaminathan, J. S., and Karplus, M., 1983. J. Comp. Chem., 4:187–217.
44. Binkley, J. S., Pople, J. A., and Hehre, W. J., 1980. J. Amer. Chem. Soc., 102:939
45. Hehre, W. J., Ditchfield, R., and Pople, J. A., 1972. J. Chem. Phys., 56:2257
46. Frisch, M. J., 1995. Gaussian Vol. 94, Pittsburgh, PA:Gaussian, Ine. Editors
47. Moller, C., and Plesset, M. S., 1934. Phys. Rev., 46:618
48. Cheatham, T. E., III and Kollman, P. A., 1998. Structure, motion, interactions and expression of bio logical macromolecules. Edited by:Sarma, M., and Sarma, R., 99–116. Schenectady, NY:Adenine Press.
49. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., and Haak, J. R., 1984. J. Comp. Phys., 81:3684–3690.
50. Andersen, H. C., 1980. J. Chem. Phys., 72:2384–2393.
51. Nose, S., and Klein, M. L., 1983. Mol. Phys., 50:1055–1076.
52. Hoover, W. G., 1985. Phys. Rev. A, 31:1695–1697.
53. Feller, S. E., Zhang, Y., Pastor, W., and Brooks, B. R., 1995. J. Chem. Phys., 103:4613–4621.
54. Prive, G. G., Yanagi, K., and Dickerson, R. E., 1991. J. Mol. Biol., 217:177–199.
55. Ravishanker, G., Swaminathan, S., Beveridge, D. L., Lavery, R., and Sklenar, H., 1989. J. Biomol. Struct. Dyn., 6:669–699.
56. Lavery, R., and Sklenar, H., 1988. J. Biomol. Struct. Dyn., 6:63–91.
57. Ferrin, T. E., Huang, C. C., Jarvis, L. E., and Langridge, R., 1988. J. Mol. Graphics, 6:13–27.
58. Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W., Kennard, O., von Kitzing, E., Lavery, R., Nelson, H. C. M., Olson, W. K., Saenger, W., Shakked, Z., Sklenar, H., Soumpasis, D. M., Tung, C. S., Wang, A. H., and Zhurkin, V. B., 1989. Nuc. Acids Res., 17:1797–1803.
59. Altona, C., and Sundaralingam, M., 1972. J. Amer. Chem. Soc., 94:8205–8212.
60. Jalluri, R. K., Yuh, Y. H., and Taylor, E. W., 1993. Anomeric effect and associated stereoelectronic effects Edited by:Thatcher, G. R.J., 277–293. Washington):(ACS.
61. Olson, W., 1982. Topics in nucleic acid structure Edited by:Neidle, S., London:(Macmillan.
62. Caldwell, J. W., and Kollman, P. A., 1995. J. Phys. Chem., 99:6208–6219.
63. Davies, D. B., 1978. Prog. Nuc. Magn. Res. Spect., 12:135–225.
64. Ramakrishnan, B., and Sundaralingam, M., 1993. J. Biomol. Struct. Dyn., 11:11–26.
65. Gorenstein, D. G., 1994. Chem. Rev., 94:1315–1338.
66. Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A., 1993. J. Phys. Chem., 97:10269–10280.
67. Cieplak, P., Cornell, W. D., Bayly, C., and Kollman, P. A., 1995. J. Comp. Chem., 16:1357–1377.
68. Hobza, P., Kabelac, M., Sponer, J., Mejzlik, P., and Vondrasek, J., 1997. J. Comp. Chem., 18:1136–1150.
69. Jorgensen, W. L., Maxwell, D. S., and Tirado-Rives, J., 1996. J. Amer. Chem. Soc., 118:11225–11236.
70. Mackerell, A. D., Wiorkiewicz-Kuczera, J., and Karplus, M., 1995. J. Amer. Chem. Soc., 117:11946–11975.
71. MacKerell, A. D., 1998. J. Phys. Chem. B., 102:3586–3616.
72. Halgren, T. A., 1996. J. Comp. Chem., 17:490–519.
73. Allinger, N. L., 1977. J. Amer. Chem. Soc., 99:8127–8134.
74. Allinger, N. L., Yuh, Y. H., and Lii, J. H., 1989. J. Amer. Chem. Soc., 111:8551–8566.
75. Allinger, N. L., Chen, K., and Lii, J.-H., 1996. J. Comp. Chem., 17:642–668.
76. Yang, L. Q., and Pettitt, B. M., 1996. J. Phys. Chem., 100:2564–2566.
77. Norberg, J., and Nilsson, L., 1996. J. Chem. Phys., 104:6052–6057.
78. MacKerell, A. D., Jr. 1998. Molecular modeling of nucleic acids Edited by:Leontis, N. B., and Santa Lucia, J. J., 304–311. Washington):(ACS.
79. Cheatham, T. E., Srinivasan, J., Case, D. A., and Kollman, P. A., 1998. J. Biomol. Struct. Dyn., 16:265–280.