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Handbook of RNA Biochemistry

Volumn , Issue , 2008, Pages 560-576

Molecular Dynamics Simulations of RNA Systems

(2) Auffinger, Pascal a Vaiana, Andrea C a

a INST DE BIOL MOLEC ET CELLULAIRE (France)

Author keywords

Advances; Backbone; RNA systems; Simulations; Solvation

Indexed keywords

EID: 33747881376 PISSN: None EISSN: None Source Type: Book
DOI: 10.1002/9783527619504.ch34 Document Type: Chapter

Times cited : (7)

References (136)

1
- 0003634460
- ASM Press, Washington, DC
- H. Grosjean, R. Benne, Modification and Editing of RNA, ASM Press, Washington, DC, 1998.
- (1998) Modification and Editing of RNA
- Grosjean, H.¹ Benne, R.²

2
- 0002592235
- P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III, P. R. Schreiner (eds), Wiley, Chichester
- P. Auffinger, E. Westhof, in: Encyclopedia of Computational Chemistry, P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III, P. R. Schreiner (eds), Wiley, Chichester, 1998, pp. 1629-1640.
- (1998) Encyclopedia of Computational Chemistry , pp. 1629-1640
- Auffinger, P.¹ Westhof, E.²

3
- 0032054952
- P. Auffinger, E. Westhof, Curr. Opin. Struct. Biol. 1998, 8, 227-236.
- (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 227-236
- Auffinger, P.¹ Westhof, E.²

4
- 84889459253
- M. Vijayan, N. Yathindra, A. S. Kolaskar (eds), University Press, Hyderabad
- P. Auffinger, E. Westhof, in: Perspective in Structural Biology, M. Vijayan, N. Yathindra, A. S. Kolaskar (eds), University Press, Hyderabad, 1999, pp. 545-555.
- (1999) Perspective in Structural Biology , pp. 545-555
- Auffinger, P.¹ Westhof, E.²

5
- 0034027592
- M. Zacharias, Curr. Opin. Struct. Biol. 2000, 10, 311-317.
- (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 311-317
- Zacharias, M.¹

6
- 0036280718
- J. Norberg, L. Nilsson, Acc. Chem. Res. 2002, 35, 465-472.
- (2002) Acc. Chem. Res. , vol.35 , pp. 465-472
- Norberg, J.¹ Nilsson, L.²

7
- 0036286321
- E. Giudice, R. Lavery, Acc. Chem. Res. 2002, 35, 350-357.
- (2002) Acc. Chem. Res. , vol.35 , pp. 350-357
- Giudice, E.¹ Lavery, R.²

8
- 14244271476
- T. E. Cheatham, 3rd, M. A. Young, Biopolymers 2000, 56, 232-256.
- (2000) Biopolymers , vol.56 , pp. 232-256
- Cheatham III, T.E.¹ Young, M.A.²

9
- 0033654654
- T. E. Cheatham, P. A. Kollman, Annu. Rev. Phys. Chem. 2000, 51, 435-471.
- (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 435-471
- Cheatham, T.E.¹ Kollman, P.A.²

10
- 0002042326
- R. H. Sarma, M. H. Sarma (eds), Adenine Press, New York
- T. E. Cheatham, P. A. Kollman. Structure, Motion, Interaction and Expression of Biological Macromolecules: Proceedings of the Tenth Conversation, R. H. Sarma, M. H. Sarma (eds), Adenine Press, New York, 1998, pp. 99-116.
- (1998) Structure, Motion, Interaction and Expression of Biological Macromolecules: Proceedings of the Tenth Conversation , pp. 99-116
- Cheatham, T.E.¹ Kollman, P.A.²

11
- 2142813682
- W. F. van Gunsteren, H. J. C. Berendsen, Angew. Chem. Int. Ed. 1990, 29, 992-1023.
- (1990) Angew. Chem. Int. Ed. , vol.29 , pp. 992-1023
- W.F.van Gunsteren¹ Berendsen, H.J.C.²

12
- 0003451443
- Clarendon Press, Oxford
- M. P. Allen, D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
- (1987) Computer Simulation of Liquids
- Allen, M.P.¹ Tildesley, D.J.²

13
- 0003705747
- Cambridge University Press, Cambridge
- D. C. Rapaport, The Art of Molecular Dynamics Simulation, Cambridge University Press, Cambridge, 1995.
- (1995) The Art of Molecular Dynamics Simulation
- Rapaport, D.C.¹

14
- 0003927323
- J. A. McCammon, S. C. Harvey (eds), Cambridge University Press, Cambridge
- J. A. McCammon, S. C. Harvey, in: Dynamics of Proteins and Nucleic Acids, J. A. McCammon, S. C. Harvey (eds), Cambridge University Press, Cambridge, 1987.
- (1987) Dynamics of Proteins and Nucleic Acids
- McCammon, J.A.¹ Harvey, S.C.²

15
- 0003653902
- Pearson Education, Harlow
- A. R. Leach, Molecular Modelling: Principles and Applications, Pearson Education, Harlow, 2001.
- (2001) Molecular Modelling: Principles and Applications
- Leach, A.R.¹

16
- 0030918284
- T. Schlick, E. Barth, M. Mandziuk, Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 181-222.
- (1997) Annu. Rev. Biophys. Biomol. Struct. , vol.26 , pp. 181-222
- Schlick, T.¹ Barth, E.² Mandziuk, M.³

17
- 0035449971
- P. F. Batcho, D. A. Case, T. Schlick, J. Chem. Phys. 2001, 115, 4003-4018.
- (2001) J. Chem. Phys. , vol.115 , pp. 4003-4018
- Batcho, P.F.¹ Case, D.A.² Schlick, T.³

18
- 0034892788
- T. Schlick, Structure 2001, 9, R45-R53.
- (2001) Structure , vol.9
- Schlick, T.¹

19
- 0034725528
- P. Auffinger, E. Westhof, J. Mol. Biol. 2000, 300, 1113-1131.
- (2000) J. Mol. Biol. , vol.300 , pp. 1113-1131
- Auffinger, P.¹ Westhof, E.²

20
- 0035793219
- P. Auffinger, E. Westhof, J. Mol. Biol. 2001, 305, 1057-1072.
- (2001) J. Mol. Biol. , vol.305 , pp. 1057-1072
- Auffinger, P.¹ Westhof, E.²

21
- 0030953141
- T. E. Cheatham, P. A. Kollman, J. Am. Chem. Soc. 1997, 119, 4805-4825.
- (1997) J. Am. Chem. Soc. , vol.119 , pp. 4805-4825
- Cheatham, T.E.¹ Kollman, P.A.²

22
- 0035905574
- P. Auffinger, E. Westhof, Angew. Chem. Int Ed. 2001, 40, 4648-4650.
- (2001) Angew. Chem. Int Ed. , vol.40 , pp. 4648-4650
- Auffinger, P.¹ Westhof, E.²

23
- 0034185360
- K. Kulinska, T. Kulinski, A. Lyubartsev, A. Laaksonen, R. W. Adamiak, Comp. Chem. 2000, 24, 451-457.
- (2000) Comp. Chem. , vol.24 , pp. 451-457
- Kulinska, K.¹ Kulinski, T.² Lyubartsev, A.³ Laaksonen, A.⁴ Adamiak, R.W.⁵

24
- 0034235396
- M. C. Nagan, P. Beuning, K. Musier-Forsyth, C. J. Cramer, Nucleic Acids Res. 2000, 28, 2527-2534.
- (2000) Nucleic Acids Res. , vol.28 , pp. 2527-2534
- Nagan, M.C.¹ Beuning, P.² Musier-Forsyth, K.³ Cramer, C.J.⁴

25
- 0033581172
- M. C. Nagan, S. S. Kerimo, K. Musierforsyth, C. J. Cramer, J. Am. Chem. Soc. 1999, 121, 7310-7317.
- (1999) J. Am. Chem. Soc. , vol.121 , pp. 7310-7317
- Nagan, M.C.¹ Kerimo, S.S.² Musierforsyth, K.³ Cramer, C.J.⁴

26
- 0034545696
- C. Schneider, J. Suhnel, J. Biomol. Struct. Dyn. 2000, 18, 345-352.
- (2000) J. Biomol. Struct. Dyn. , vol.18 , pp. 345-352
- Schneider, C.¹ Suhnel, J.²

27
- 0037187796
- M. Sundaralingam, B. Pan, Biophys. Chem. 2002, 95, 273-282.
- (2002) Biophys. Chem. , vol.95 , pp. 273-282
- Sundaralingam, M.¹ Pan, B.²

28
- 0036009329
- M. Egli, Chem. Biol. 2002, 9, 277-286.
- (2002) Chem. Biol. , vol.9 , pp. 277-286
- Egli, M.¹

29
- 0036077305
- H. M. Berman, J. Westbrook, Z. Feng, L. Iype, B. Schneider, C. Zardecki, Acta Crystallogr. D 2002, 58, 889-898.
- (2002) Acta Crystallogr. D , vol.58 , pp. 889-898
- Berman, H.M.¹ Westbrook, J.² Feng, Z.³ Iype, L.⁴ Schneider, B.⁵ Zardecki, C.⁶

30
- 0036616218
- H. M. Berman, T. Battistuz, T. N. Bhat, W. F. Bluhm, P. E. Bourne, K. Burkhardt, Z. Feng, G. L. Gilliland, L. Iype, S. Jain et al., Acta Crystallogr. D 2002, 58, 899-907.
- (2002) Acta Crystallogr. D , vol.58 , pp. 899-907
- Berman, H.M.¹ Battistuz, T.² Bhat, T.N.³ Bluhm, W.F.⁴ Bourne, P.E.⁵ Burkhardt, K.⁶ Feng, Z.⁷ Gilliland, G.L.⁸ Iype, L.⁹ Jain, S.¹⁰

31
- 0029017638
- K. McDonald, J. M. Thornton, Prot. Eng. 1995, 8, 217-224.
- (1995) Prot. Eng. , vol.8 , pp. 217-224
- McDonald, K.¹ Thornton, J.M.²

32
- 0037441653
- S. C. Lovell, I. W. Davis, W. B. Arendall, 3rd, P. I. de Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, D. C. Richardson, Proteins 2003, 50, 437-450.
- (2003) Proteins , vol.50 , pp. 437-450
- Lovell, S.C.¹ Davis, I.W.² Arendall III, W.B.³ De Bakker, P.I.⁴ Word, J.M.⁵ Prisant, M.G.⁶ Richardson, J.S.⁷ Richardson, D.C.⁸

33
- 0000643212
- H. Grosjean, R. Benne (eds), American Society for Microbiology, Washington, DC
- P. Auffinger, E. Westhof, in: Modification and Editing of RNA, H. Grosjean, R. Benne (eds), American Society for Microbiology, Washington, DC, 1998, pp. 103-112.
- (1998) Modification and Editing of RNA , pp. 103-112
- Auffinger, P.¹ Westhof, E.²

34
- 0035834495
- Csaszar, N. Spackova, R. Stefl, J. Sponer, N. B. Leontis, J. Mol. Biol. 2001, 313, 1073-1091.
- (2001) J. Mol. Biol. , vol.313 , pp. 1073-1091
- Spackova, C.N.¹ Stefl, R.² Sponer, J.³ Leontis, N.B.⁴

35
- 0037424612
- M. Kaul, C. M. Barbieri, J. E. Kerrigan, D. S. Pilch, J. Mol. Biol. 2003, 326, 1373-1387.
- (2003) J. Mol. Biol. , vol.326 , pp. 1373-1387
- Kaul, M.¹ Barbieri, C.M.² Kerrigan, J.E.³ Pilch, D.S.⁴

36
- 0041335577
- D. S. Pilch, M. Kaul, C. M. Barbieri, J. E. Kerrigan, Biopolymers 2003, 70, 58-79.
- (2003) Biopolymers , vol.70 , pp. 58-79
- Pilch, D.S.¹ Kaul, M.² Barbieri, C.M.³ Kerrigan, J.E.⁴

37
- 0034989056
- U. Das, S. Chen, M. Fuxreiter, A. A. Vaguine, J. Richelle, H. M. Berman, S. J. Wodak, Acta Crystallogr. D 2001, 57, 813-828.
- (2001) Acta Crystallogr. D , vol.57 , pp. 813-828
- Das, U.¹ Chen, S.² Fuxreiter, M.³ Vaguine, A.A.⁴ Richelle, J.⁵ Berman, H.M.⁶ Wodak, S.J.⁷

38
- 1542498400
- P. Auffinger, L. Bielecki, E. Westhof, Structure 2004, 12, 379-388.
- (2004) Structure , vol.12 , pp. 379-388
- Auffinger, P.¹ Bielecki, L.² Westhof, E.³

39
- 0029845690
- Hutter, P. Carloni, M. Parrinello, J. Am. Chem. Soc. 1996, 118, 8710-8712.
- (1996) J. Am. Chem. Soc. , vol.118 , pp. 8710-8712
- Carloni, H.P.¹ Parrinello, M.²

40
- 0034036155
- D. R. Bevan, L. Li, L. G. Pedersen, T. A. Darden, Biophys. J. 2000, 78, 668-682.
- (2000) Biophys. J. , vol.78 , pp. 668-682
- Bevan, D.R.¹ Li, L.² Pedersen, L.G.³ Darden, T.A.⁴

41
- 0001628106
- H. Lee, T. A. Darden, L. G. Pedersen, J. Chem. Phys. 1995, 102, 3830-3834.
- (1995) J. Chem. Phys. , vol.102 , pp. 3830-3834
- Lee, H.¹ Darden, T.A.² Pedersen, L.G.³

42
- 0029110156
- D. M. York, W. Yang, H. Lee, T. Darden, L. G. Pedersen, J. Am. Chem. Soc. 1995, 117, 5001-5002.
- (1995) J. Am. Chem. Soc. , vol.117 , pp. 5001-5002
- York, D.M.¹ Yang, W.² Lee, H.³ Darden, T.⁴ Pedersen, L.G.⁵

43
- 0036106375
- N. Korolev, A. P. Lyubartsev, A. Laaksonen, L. Nordenskiold, Biophys. J. 2002, 82, 2860-2875.
- (2002) Biophys. J. , vol.82 , pp. 2860-2875
- Korolev, N.¹ Lyubartsev, A.P.² Laaksonen, A.³ Nordenskiold, L.⁴

44
- 4243785712
- H. Lee, T. Darden, L. Pedersen, Chem. Phys. Lett. 1995, 243, 229-235.
- (1995) Chem. Phys. Lett. , vol.243 , pp. 229-235
- Lee, H.¹ Darden, T.² Pedersen, L.³

45
- 0037061982
- Nina, T. Simonson, J. Phys. Chem. B 2002, 106, 3696-3705.
- (2002) J. Phys. Chem. B , vol.106 , pp. 3696-3705
- Nina, T.S.¹

46
- 67049156092
- H. Ohtaki, Monatsh. Chem. 2001, 132, 1237-1268.
- (2001) Monatsh. Chem. , vol.132 , pp. 1237-1268
- Ohtaki, H.¹

47
- 0142025560
- H. Ohtaki, T. Radnai, Chem. Rev. 1993, 93, 1157-1204.
- (1993) Chem. Rev. , vol.93 , pp. 1157-1204
- Ohtaki, H.¹ Radnai, T.²

48
- 0346366808
- P. Auffinger, L. Bielecki, E. Westhof, J. Mol. Biol. 2004, 335, 555-571.
- (2004) J. Mol. Biol. , vol.335 , pp. 555-571
- Auffinger, P.¹ Bielecki, L.² Westhof, E.³

49
- 0038539610
- P. Auffinger, L. Bielecki, E. Westhof, Chem. Biol. 2003, 10, 551-561.
- (2003) Chem. Biol. , vol.10 , pp. 551-561
- Auffinger, P.¹ Bielecki, L.² Westhof, E.³

50
- 0037764044
- K. Reblova, N. Spackova, R. Stefl, K. Csaszar, J. Koca, N. B. Leontis, J. Sponer, Biophys. J. 2003, 84, 3564-3582.
- (2003) Biophys. J. , vol.84 , pp. 3564-3582
- Reblova, K.¹ Spackova, N.² Stefl, R.³ Csaszar, K.⁴ Koca, J.⁵ Leontis, N.B.⁶ Sponer, J.⁷

51
- 0031915278
- T. Hermann, P. Auffinger, E. Westhof, Eur. J. Biophys. 1998, 27, 153-165.
- (1998) Eur. J. Biophys. , vol.27 , pp. 153-165
- Hermann, T.¹ Auffinger, P.² Westhof, E.³

52
- 17944388579
- K. Reblova, N. Spackova, J. E. Sponer, J. Koca, J. Sponer, Nucleic Acids Res 2003, 31, 6942-6952.
- (2003) Nucleic Acids Res , vol.31 , pp. 6942-6952
- Reblova, K.¹ Spackova, N.² Sponer, J.E.³ Koca, J.⁴ Sponer, J.⁵

53
- 0029633186
- D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, S. DeBolt, D. Ferguson, G. Seibel, P. Kollman, Comp. Phys. Commun. 1995, 91, 1-41.
- (1995) Comp. Phys. Commun. , vol.91 , pp. 1-41
- Pearlman, D.A.¹ Case, D.A.² Caldwell, J.W.³ Ross, W.S.⁴ Cheatham, T.E.⁵ DeBolt, S.⁶ Ferguson, D.⁷ Seibel, G.⁸ Kollman, P.⁹

54
- 0008819754
- W. R. P. Scott, P. H. Hünenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krüger, W. F. van Gunsteren, J. Phys. Chem. A 1999, 103, 3596-3607.
- (1999) J. Phys. Chem. A , vol.103 , pp. 3596-3607
- Scott, W.R.P.¹ Hünenberger, P.H.² Tironi, I.G.³ Mark, A.E.⁴ Billeter, S.R.⁵ Fennen, J.⁶ Torda, A.E.⁷ Huber, T.⁸ Krüger, P.⁹ Van Gunsteren, W.F.¹⁰

55
- 0042415783
- Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, K. Schulten, J. Comput. Phys. 1999, 151, 283-312.
- (1999) J. Comput. Phys. , vol.151 , pp. 283-312
- Skeel, K.R.¹ Bhandarkar, M.² Brunner, R.³ Gursoy, A.⁴ Krawetz, N.⁵ Phillips, J.⁶ Shinozaki, A.⁷ Varadarajan, K.⁸ Schulten, K.⁹

56
- 0029011701
- W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwel, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 5179-5197.
- (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
- Cornell, W.D.¹ Cieplak, P.² Bayly, C.I.³ Gould, I.R.⁴ Merz, K.M.⁵ Ferguson, D.M.⁶ Spellmeyer, D.C.⁷ Fox, T.⁸ Caldwel, J.W.⁹ Kollman, P.A.¹⁰

57
- 84889287053
- Foloppe, A. D. MacKerell, J. Comput. Chem. 2000, 21, 88-104.
- (2000) J. Comput. Chem. , vol.21 , pp. 88-104
- Foloppe, A.D.M.¹

58
- 0000214231
- A. D. MacKerell, N. Banavali, J. Comput. Chem. 2000, 21, 105-120.
- (2000) J. Comput. Chem. , vol.21 , pp. 105-120
- MacKerell, A.D.¹ Banavali, N.²

59
- 0032459726
- D. R. Langley, J. Biomol. Struct. Dyn. 1998, 16, 487-509.
- (1998) J. Biomol. Struct. Dyn. , vol.16 , pp. 487-509
- Langley, D.R.¹

60
- 0035913529
- G. A. Kaminski, R. A. Friesner, J. Tirado-Rives, W. L. Jorgensen, J. Phys. Chem. B 2001, 105, 6474-6487.
- (2001) J. Phys. Chem. B , vol.105 , pp. 6474-6487
- Kaminski, G.A.¹ Friesner, R.A.² Tirado-Rives, J.³ Jorgensen, W.L.⁴

61
- 0031237692
- M. Feig, B. M. Pettitt, J. Chem. Phys. B 1997, 101, 7361-7363.
- (1997) J. Chem. Phys. B , vol.101 , pp. 7361-7363
- Feig, M.¹ Pettitt, B.M.²

62
- 0031808069
- M. Feig, B. M. Pettitt, Biophys. J. 1998, 75, 134-149.
- (1998) Biophys. J. , vol.75 , pp. 134-149
- Feig, M.¹ Pettitt, B.M.²

63
- 0032922174
- T. E. Cheatham, P. Cieplak, P. A. Kollman, J. Biomol. Struct. Dyn. 1999, 16, 845-862.
- (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845-862
- Cheatham, T.E.¹ Cieplak, P.² Kollman, P.A.³

64
- 0037342509
- S. Y. Reddy, F. Leclerc, M. Karplus, Biophys. J. 2003, 84, 1421-1449.
- (2003) Biophys. J. , vol.84 , pp. 1421-1449
- Reddy, S.Y.¹ Leclerc, F.² Karplus, M.³

65
- 0035312821
- T. A. Halgren, W. Damm, Curr. Opin. Struct. Biol. 2001, 11, 236-242.
- (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 236-242
- Halgren, T.A.¹ Damm, W.²

66
- 0001772690
- K. B. Lipkowitz, D. B. Boyd (eds), VCH, New York
- U. Dinur, A. T. Hagler, in: Reviews in Computational Chemistry, K. B. Lipkowitz, D. B. Boyd (eds), VCH, New York, 1991, pp. 99-164.
- (1991) Reviews in Computational Chemistry , pp. 99-164
- Dinur, U.¹ Hagler, A.T.²

67
- 0035451865
- J. Wang, P. Kollman, J. Comput. Chem. 2001, 22, 1219-1228.
- (2001) J. Comput. Chem. , vol.22 , pp. 1219-1228
- Wang, J.¹ Kollman, P.²

68
- 0001628105
- S. L. Njo, W. F. van Gunsteren, F. Muller-Plathe, J. Chem. Phys. 1995, 102, 6199-6207.
- (1995) J. Chem. Phys. , vol.102 , pp. 6199-6207
- Njo, S.L.¹ Van Gunsteren, W.F.² Muller-Plathe, F.³

69
- 0141789943
- A. C. Vaiana, A. Schulz, J. Wolfrum, M. Sauer, J. C. Smith, J. Comput. Chem. 2003, 24, 632-639.
- (2003) J. Comput. Chem. , vol.24 , pp. 632-639
- Vaiana, A.C.¹ Schulz, A.² Wolfrum, J.³ Sauer, M.⁴ Smith, J.C.⁵

70
- 0037202434
- D. Kony, W. Damm, S. Stoll, W. F. Van Gunsteren, J. Comput. Chem. 2002, 23, 1416-1429.
- (2002) J. Comput. Chem. , vol.23 , pp. 1416-1429
- Kony, D.¹ Damm, W.² Stoll, S.³ Van Gunsteren, W.F.⁴

71
- 0003045884
- C. J. M. Huige, C. Altona, J. Comput. Chem. 1995, 16, 56-79.
- (1995) J. Comput. Chem. , vol.16 , pp. 56-79
- Huige, C.J.M.¹ Altona, C.²

72
- 0037495965
- K. L. Meagher, L. T. Redman, H. A. Carlson, J. Comput. Chem. 2003, 24, 1016-1025.
- (2003) J. Comput. Chem. , vol.24 , pp. 1016-1025
- Meagher, K.L.¹ Redman, L.T.² Carlson, H.A.³

73
- 0004016501
- W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926-936.
- (1983) J. Chem. Phys. , vol.79 , pp. 926-936
- Jorgensen, W.L.¹ Chandrasekhar, J.² Madura, J.D.³ Impey, R.W.⁴ Klein, M.L.⁵

74
- 0000020246
- M. W. Mahoney, W. L. Jorgensen, J. Chem. Phys. 2000, 112, 8910-8922.
- (2000) J. Chem. Phys. , vol.112 , pp. 8910-8922
- Mahoney, M.W.¹ Jorgensen, W.L.²

75
- 0002775934
- B. Pullman (ed.), Reidel, Dordrecht
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, J. Hermans, in: Intermolecular Forces, B. Pullman (ed.), Reidel, Dordrecht, 1981, pp. 331-342.
- (1981) Intermolecular Forces , pp. 331-342
- Berendsen, H.J.C.¹ Postma, J.P.M.² Van Gunsteren, W.F.³ Hermans, J.⁴

76
- 1242346370
- H. J. C. Berendsen, J. R. Grigera, T. P. Straatsma, J. Phys. Chem. 1987, 97, 6269-6271.
- (1987) J. Phys. Chem. , vol.97 , pp. 6269-6271
- Berendsen, H.J.C.¹ Grigera, J.R.² Straatsma, T.P.³

77
- 0033637521
- M. Tarek, D. J. Tobias, Biophys. J. 2000, 79, 3244-3257.
- (2000) Biophys. J. , vol.79 , pp. 3244-3257
- Tarek, M.¹ Tobias, D.J.²

78
- 0000828880
- Auffinger, D. L. Beveridge, Chem. Phys. Lett. 1995, 234, 413-415.
- (1995) Chem. Phys. Lett. , vol.234 , pp. 413-415
- Auffinger, D.L.B.¹

79
- 0031516150
- K. B. Lipkowitz, D. B. Boyd (eds), VCH, New York
- G. Ravishanker, P. Auffinger, D. R. Langley, B. Jayaram, M. A. Young, D. L. Beveridge, in: Reviews in Computational Chemistry, K. B. Lipkowitz, D. B. Boyd (eds), VCH, New York, 1997, pp. 317-372.
- (1997) Reviews in Computational Chemistry , pp. 317-372
- Ravishanker, G.¹ Auffinger, P.² Langley, D.R.³ Jayaram, B.⁴ Young, M.A.⁵ Beveridge, D.L.⁶

80
- 0030005364
- S. Louise-May, P. Auffinger, E. Westhof, Curr. Opin. Struct. Biol. 1996, 6, 289-298.
- (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 289-298
- Louise-May, S.¹ Auffinger, P.² Westhof, E.³

81
- 0033024177
- C. Sagui, T. A. Darden, Annu. Rev. Biophys. Struct. 1999, 28, 155-179.
- (1999) Annu. Rev. Biophys. Struct. , vol.28 , pp. 155-179
- Sagui, C.¹ Darden, T.A.²

82
- 0033104039
- T. Darden, L. Perera, P. Li, L. Pedersen, Structure 1999, 7, R55-R60.
- (1999) Structure , vol.7
- Darden, T.¹ Perera, L.² Li, P.³ Pedersen, L.⁴

83
- 0029170114
- T. E. Cheatham, J. L. Miller, T. Fox, T. A. Darden, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 4193-4194.
- (1995) J. Am. Chem. Soc. , vol.117 , pp. 4193-4194
- Cheatham, T.E.¹ Miller, J.L.² Fox, T.³ Darden, T.A.⁴ Kollman, P.A.⁵

84
- 33750587438
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, J. Chem. Phys. 1984, 81, 3684-3690.
- (1984) J. Chem. Phys. , vol.81 , pp. 3684-3690
- Berendsen, H.J.C.¹ Postma, J.P.M.² Van Gunsteren, W.F.³ DiNola, A.⁴

85
- 0037187806
- P. Auffinger, E. Westhof, Biophys. Chem. 2002, 95, 203-210.
- (2002) Biophys. Chem. , vol.95 , pp. 203-210
- Auffinger, P.¹ Westhof, E.²

86
- 33646940952
- J. P. Ryckaert, G. Ciccotti, H. J. C. Berendsen, J. Comput. Phys. 1977, 23, 327-336.
- (1977) J. Comput. Phys. , vol.23 , pp. 327-336
- Ryckaert, J.P.¹ Ciccotti, G.² Berendsen, H.J.C.³

87
- 0001430231
- S. C. Harvey, R. K. Z. Tan, T. E. Cheatham, J. Comput. Chem. 1998, 19, 726-740.
- (1998) J. Comput. Chem. , vol.19 , pp. 726-740
- Harvey, S.C.¹ Tan, R.K.Z.² Cheatham, T.E.³

88
- 0000094135
- S. W. Chiu, M. Clark, S. Subramaniam, E. Jakobsson, J. Computat. Chem. 2000, 21, 121-131.
- (2000) J. Computat. Chem. , vol.21 , pp. 121-131
- Chiu, S.W.¹ Clark, M.² Subramaniam, S.³ Jakobsson, E.⁴

89
- 0030723027
- P. Auffinger, E. Westhof, J. Mol. Biol. 1997, 274, 54-63.
- (1997) J. Mol. Biol. , vol.274 , pp. 54-63
- Auffinger, P.¹ Westhof, E.²

90
- 0032907143
- P. Auffinger, S. Louise-May, E. Westhof, Biophys. J. 1999, 76, 50-64.
- (1999) Biophys. J. , vol.76 , pp. 50-64
- Auffinger, P.¹ Louise-May, S.² Westhof, E.³

91
- 0028869415
- P. Auffinger, S. Louise-May, E. Westhof, J. Am. Chem. Soc. 1995, 117, 6720-6726.
- (1995) J. Am. Chem. Soc. , vol.117 , pp. 6720-6726
- Auffinger, P.¹ Louise-May, S.² Westhof, E.³

92
- 0029911794
- P. Auffinger, S. Louise-May, E. Westhof, J. Am. Chem. Soc. 1996, 118, 1181-1189.
- (1996) J. Am. Chem. Soc. , vol.118 , pp. 1181-1189
- Auffinger, P.¹ Louise-May, S.² Westhof, E.³

93
- 0029776466
- P. Auffinger, E. Westhof, Biophys. J. 1996, 71, 940-954.
- (1996) Biophys. J. , vol.71 , pp. 940-954
- Auffinger, P.¹ Westhof, E.²

94
- 0031566427
- P. Auffinger, E. Westhof, J. Mol. Biol. 1997, 269, 326-341.
- (1997) J. Mol. Biol. , vol.269 , pp. 326-341
- Auffinger, P.¹ Westhof, E.²

95
- 0030670359
- M. Braxenthaler, R. Unger, D. Auerbach, J. A. Given, J. Moult, Proteins 1997, 29, 417-425.
- (1997) Proteins , vol.29 , pp. 417-425
- Braxenthaler, M.¹ Unger, R.² Auerbach, D.³ Given, J.A.⁴ Moult, J.⁵

96
- 0031910020
- L. S. D. Caves, J. D. Evanseck, M. Karplus, Prot. Sci. 1998, 7, 649-666.
- (1998) Prot. Sci. , vol.7 , pp. 649-666
- Caves, L.S.D.¹ Evanseck, J.D.² Karplus, M.³

97
- 0030134514
- H.-B. Zhou, L. Wang, J. Phys. Chem. 1996, 100, 8101-8105.
- (1996) J. Phys. Chem. , vol.100 , pp. 8101-8105
- Zhou, H.-B.¹ Wang, L.²

98
- 0001349174
- W. F. van Gunsteren, A. E. Mark, J. Chem. Phys. 1998, 108, 6109-6116.
- (1998) J. Chem. Phys. , vol.108 , pp. 6109-6116
- W.F.van Gunsteren¹ Mark, A.E.²

99
- 0000930430
- Swaminathan, G. Ravishanker, D. L. Beveridge, J. Am. Chem. Soc. 1991, 111, 5027-5040.
- (1991) J. Am. Chem. Soc. , vol.111 , pp. 5027-5040
- Ravishanker, S.G.¹ Beveridge, D.L.²

100
- 14244271781
- P. Auffinger, E. Westhof, Biopolymers 2000, 56, 266-274.
- (2000) Biopolymers , vol.56 , pp. 266-274
- Auffinger, P.¹ Westhof, E.²

101
- 0024539180
- Lavery, H. Sklenar, J. Biomol. Struct. Dyn. 1989, 6, 655-667.
- (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 655-667
- Lavery, H.S.¹

102
- 0242396923
- X. J. Lu, W. K. Olson, Nucleic Acids Res. 2003, 31, 5108-5121.
- (2003) Nucleic Acids Res. , vol.31 , pp. 5108-5121
- Lu, X.J.¹ Olson, W.K.²

103
- 0002897580
- Y. H. Ross, R. B. Leslie, P. J. Lillford (eds), Technomic, Basel
- P. Auffinger, E. Westhof, in: Water Management in the Design and Distribution of Quality Food, Y. H. Ross, R. B. Leslie, P. J. Lillford (eds), Technomic, Basel, 1999, pp. 165-198.
- (1999) Water Management in the Design and Distribution of Quality Food , pp. 165-198
- Auffinger, P.¹ Westhof, E.²

104
- 0006627150
- M. Feig, B. M. Pettitt, Biopolymers 1998, 48, 199-209.
- (1998) Biopolymers , vol.48 , pp. 199-209
- Feig, M.¹ Pettitt, B.M.²

105
- 0036286851
- V. A. Makarov, B. M. Pettitt, M. Feig, Acc. Chem. Res. 2002, 35, 376-384.
- (2002) Acc. Chem. Res. , vol.35 , pp. 376-384
- Makarov, V.A.¹ Pettitt, B.M.² Feig, M.³

106
- 0345924974
- T. Schlick, H. H. Gan (eds), Springer Verlag, Heidelberg
- P. Auffinger, B. Masquida, E. Westhof, in: Computational Methods for Macromolecules: Challenges and Applications, T. Schlick, H. H. Gan (eds), Springer Verlag, Heidelberg, 2002, pp. 61-70.
- (2002) Computational Methods for Macromolecules: Challenges and Applications , pp. 61-70
- Auffinger, P.¹ Masquida, B.² Westhof, E.³

107
- 0032838372
- Y. Tang, L. Nilsson, Biophys. J. 1999, 77, 1284-1305.
- (1999) Biophys. J. , vol.77 , pp. 1284-1305
- Tang, Y.¹ Nilsson, L.²

108
- 0033729881
- A. Lahiri, L. Nilsson, Biophys. J. 2000, 79, 2276-2289.
- (2000) Biophys. J. , vol.79 , pp. 2276-2289
- Lahiri, A.¹ Nilsson, L.²

109
- 0033855843
- J. Sarzynska, T. Kulinski, L. Nilsson, Biophys. J. 2000, 79, 1213-1227.
- (2000) Biophys. J. , vol.79 , pp. 1213-1227
- Sarzynska, J.¹ Kulinski, T.² Nilsson, L.³

110
- 0000367525
- J. Norberg, L. Nilsson, J. Chem. Phys. 1996, 104, 6052-6057.
- (1996) J. Chem. Phys. , vol.104 , pp. 6052-6057
- Norberg, J.¹ Nilsson, L.²

111
- 0034725383
- R. Soliva, E. Sherer, F. J. Luque, C. A. Laughton, M. Orozco, J. Am. Chem. Soc. 2000, 122, 5997-6008.
- (2000) J. Am. Chem. Soc. , vol.122 , pp. 5997-6008
- Soliva, R.¹ Sherer, E.² Luque, F.J.³ Laughton, C.A.⁴ Orozco, M.⁵

112
- 0032503508
- H. De Winter, E. Lescrinier, A. Van Aerschot, P. Herdewijn, J. Am. Chem. Soc. 1998, 120, 5381-5394.
- (1998) J. Am. Chem. Soc. , vol.120 , pp. 5381-5394
- De Winter, H.¹ Lescrinier, E.² Van Aerschot, A.³ Herdewijn, P.⁴

113
- 0032529640
- K. E. Lind, V. Mohan, M. Manoharan, D. M. Ferguson, Nucleic Acids Res. 1998, 26, 3694-3799.
- (1998) Nucleic Acids Res. , vol.26 , pp. 3694-3799
- Lind, K.E.¹ Mohan, V.² Manoharan, M.³ Ferguson, D.M.⁴

114
- 0346882954
- Y. Pan, A. D. MacKerell, Nucleic Acids Res. 2003, 31, 7131-7140.
- (2003) Nucleic Acids Res. , vol.31 , pp. 7131-7140
- Pan, Y.¹ MacKerell, A.D.²

115
- 0344119523
- J. Sarzynska, L. Nilsson, T. Kulinski, Biophys J 2003, 85, 3445-3459.
- (2003) Biophys J , vol.85 , pp. 3445-3459
- Sarzynska, J.¹ Nilsson, L.² Kulinski, T.³

116
- 0037114646
- F. Pitici, D. L. Beveridge, A. M. Baranger, Biopolymers 2002, 65, 424-435.
- (2002) Biopolymers , vol.65 , pp. 424-435
- Pitici, F.¹ Beveridge, D.L.² Baranger, A.M.³

117
- 0034538789
- J. Guo, I. Daizadeh, W. H. Gmeiner, J. Biomol. Struct. Dyn. 2000, 18, 335-344.
- (2000) J. Biomol. Struct. Dyn. , vol.18 , pp. 335-344
- Guo, J.¹ Daizadeh, I.² Gmeiner, W.H.³

118
- 0035951296
- C. Schneider, M. Brandl, J. Sühnel, J. Mol. Biol. 2001, 305, 659-667.
- (2001) J. Mol. Biol. , vol.305 , pp. 659-667
- Schneider, C.¹ Brandl, M.² Sühnel, J.³

119
- 0030320856
- P. Auffinger, S. Louise-May, E. Westhof, Faraday Discuss. 1996, 103, 151-174.
- (1996) Faraday Discuss. , vol.103 , pp. 151-174
- Auffinger, P.¹ Louise-May, S.² Westhof, E.³

120
- 0037440163
- W. Li, B. Ma, B. A. Shapiro, Nucleic Acids Res. 2003, 31, 629-638.
- (2003) Nucleic Acids Res. , vol.31 , pp. 629-638
- Li, W.¹ Ma, B.² Shapiro, B.A.³

121
- 0032530132
- R. A. Torres, T. C. Bruice, Proc. Natl. Acad. Sci. USA 1998, 95, 11077-11082.
- (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 11077-11082
- Torres, R.A.¹ Bruice, T.C.²

122
- 0034624405
- R. A. Torres, T. C. Bruice, J. Am Chem. Soc. 2000, 122, 781-791.
- (2000) J. Am Chem. Soc. , vol.122 , pp. 781-791
- Torres, R.A.¹ Bruice, T.C.²

123
- 0030849184
- Hermann, P. Auffinger, W. G. Scott, E. Westhof, Nucleic Acids Res. 1997, 25, 3421-3427.
- (1997) Nucleic Acids Res. , vol.25 , pp. 3421-3427
- Auffinger, H.P.¹ Scott, W.G.² Westhof, E.³

124
- 0037112601
- J. L. Asensio, A. Hidalgo, I. Cuesta, C. Gonzalez, J. Canada, C. Vicent, J. L. Chiara, G. Cuevas, J. Jimenez-Barbero, Chemistry 2002, 8, 5228-5240.
- (2002) Chemistry , vol.8 , pp. 5228-5240
- Asensio, J.L.¹ Hidalgo, A.² Cuesta, I.³ Gonzalez, C.⁴ Canada, J.⁵ Vicent, C.⁶ Chiara, J.L.⁷ Cuevas, G.⁸ Jimenez-Barbero, J.⁹

125
- 0033057703
- C. M. Reyes, P. A. Kollman, RNA 1999, 5, 235-244.
- (1999) RNA , vol.5 , pp. 235-244
- Reyes, C.M.¹ Kollman, P.A.²

126
- 0033010186
- Hermann, E. Westhof, Nat. Struct. Biol. 1999, 6, 540-544.
- (1999) Nat. Struct. Biol. , vol.6 , pp. 540-544
- Hermann, E.W.¹

127
- 0034901809
- J. Guo, W. H. Gmeiner, Biophys. J. 2001, 81, 630-642.
- (2001) Biophys. J. , vol.81 , pp. 630-642
- Guo, J.¹ Gmeiner, W.H.²

128
- 0029109915
- D. A. Zichi, J. Am. Chem. Soc. 1995, 117, 2957-2969.
- (1995) J. Am. Chem. Soc. , vol.117 , pp. 2957-2969
- Zichi, D.A.¹

129
- 0031577316
- J. Miller, P. A. Kollman, J. Mol. Biol. 1997, 270, 436-450.
- (1997) J. Mol. Biol. , vol.270 , pp. 436-450
- Miller, J.¹ Kollman, P.A.²

130
- 0036975258
- F. Kieken, E. Arnoult, F. Barbault, F. Paquet, T. Huynh-Dinh, J. Paoletti, D. Genest, G. Lancelot, Eur. Biophys. J. 2002, 31, 521-531.
- (2002) Eur. Biophys. J. , vol.31 , pp. 521-531
- Kieken, F.¹ Arnoult, E.² Barbault, F.³ Paquet, F.⁴ Huynh-Dinh, T.⁵ Paoletti, J.⁶ Genest, D.⁷ Lancelot, G.⁸

131
- 0037698928
- G. La Penna, D. Genest, A. Perico, Biopolymers 2003, 69, 1-14.
- (2003) Biopolymers , vol.69 , pp. 1-14
- La Penna, G.¹ Genest, D.² Perico, A.³

132
- 0141643186
- T. Kulinski, M. Olejniczak, H. Huthoff, L. Bielecki, K. Pachulska-Wieczorek, A. T. Das, B. Berkhout, R. W. Adamiak, J. Biol. Chem. 2003, 278, 38892-38901.
- (2003) J. Biol. Chem. , vol.278 , pp. 38892-38901
- Kulinski, T.¹ Olejniczak, M.² Huthoff, H.³ Bielecki, L.⁴ Pachulska-Wieczorek, K.⁵ Das, A.T.⁶ Berkhout, B.⁷ Adamiak, R.W.⁸

133
- 0242317674
- F. Beaurain, C. Di Primo, J. J. Toulme, M. Laguerre, Nucleic Acids Res. 2003, 31, 4275-4284.
- (2003) Nucleic Acids Res. , vol.31 , pp. 4275-4284
- Beaurain, F.¹ Di Primo, C.² Toulme, J.J.³ Laguerre, M.⁴

134
- 0033198021
- C. Schneider, J. Sühnel, Biopolymers 1999, 50, 287-302.
- (1999) Biopolymers , vol.50 , pp. 287-302
- Schneider, C.¹ Sühnel, J.²

135
- 0034999080
- C. M. Reyes, R. Nifosi, A. D. Frankel, P. A. Kollman, Biophys. J. 2001, 80, 2833-2842.
- (2001) Biophys. J. , vol.80 , pp. 2833-2842
- Reyes, C.M.¹ Nifosi, R.² Frankel, A.D.³ Kollman, P.A.⁴

136
- 0036929346
- T. Castrignano, G. Chillemi, G. Varani, A. Desideri, Biophys. J. 2002, 83, 3542-3552.
- (2002) Biophys. J. , vol.83 , pp. 3542-3552
- Castrignano, T.¹ Chillemi, G.² Varani, G.³ Desideri, A.⁴

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