-
4
-
-
0001783322
-
-
Eckstein, F., Lilley, D. M. J., Eds.; Springer-Verlag: Berlin
-
(b) Wang A. H. In Nucleic Acids and Molecular Biology; Eckstein, F., Lilley, D. M. J., Eds.; Springer-Verlag: Berlin, 1987; Vol. 1, pp 53-69.
-
(1987)
Nucleic Acids and Molecular Biology
, vol.1
, pp. 53-69
-
-
Wang, A.H.1
-
5
-
-
0023100944
-
-
(c) Neidle, S.; Pearl, L. H.; Skelly, J. V. Biochem. J. 1987, 243, 1.
-
(1987)
Biochem. J.
, vol.243
, pp. 1
-
-
Neidle, S.1
Pearl, L.H.2
Skelly, J.V.3
-
6
-
-
4043181098
-
-
Ellis, G. P., West, G. B., Eds.; Elsevier: Amsterdam, Chapter 2
-
(d) Cheng, C. C. In Progress in Medicinal Chemistry; Ellis, G. P., West, G. B., Eds.; Elsevier: Amsterdam, 1988; Vol. 25, Chapter 2.
-
(1988)
Progress in Medicinal Chemistry
, vol.25
-
-
Cheng, C.C.1
-
11
-
-
0018143102
-
-
and references therein
-
(a) Ornstein R. L.; Rein, R.; Breen, D. L.; Macelroy, R. D. Biopolymers 1978, 17, 2341 and references therein.
-
(1978)
Biopolymers
, vol.17
, pp. 2341
-
-
Ornstein, R.L.1
Rein, R.2
Breen, D.L.3
Macelroy, R.D.4
-
13
-
-
84984051896
-
-
(c) Langlet, J.; Claverie, P.; Caron, F.; Boeuve, J. C. Int. J. Quant. Chem. 1981, 19, 299.
-
(1981)
Int. J. Quant. Chem.
, vol.19
, pp. 299
-
-
Langlet, J.1
Claverie, P.2
Caron, F.3
Boeuve, J.C.4
-
14
-
-
0021688227
-
-
(d) Haran, T. E.; Berkowich-Yellin, Z.; Shakked, Z. J. Biomol. Struct. Dyn. 1984, 2, 397.
-
(1984)
J. Biomol. Struct. Dyn.
, vol.2
, pp. 397
-
-
Haran, T.E.1
Berkowich-Yellin, Z.2
Shakked, Z.3
-
15
-
-
0023460108
-
-
(e) Srinivasan, A. R.; Torres, R.; Clark, W.; Olson, W. K. J. Biomol. Struct. Dyn. 1987, 5, 459.
-
(1987)
J. Biomol. Struct. Dyn.
, vol.5
, pp. 459
-
-
Srinivasan, A.R.1
Torres, R.2
Clark, W.3
Olson, W.K.4
-
16
-
-
0023732135
-
-
(f) Sarai, A.; Mazur, J.; Nussinov, R.; Jernigan, R. L. Biochemistry 1988, 27, 8498.
-
(1988)
Biochemistry
, vol.27
, pp. 8498
-
-
Sarai, A.1
Mazur, J.2
Nussinov, R.3
Jernigan, R.L.4
-
17
-
-
0024974069
-
-
(g) Sarai, A.; Mazur, J.; Nussinov, R.; Jernigan, R. L. Biochemistry 1989, 28, 7842.
-
(1989)
Biochemistry
, vol.28
, pp. 7842
-
-
Sarai, A.1
Mazur, J.2
Nussinov, R.3
Jernigan, R.L.4
-
30
-
-
0029167904
-
-
(e) Hobza, P.: Sponer, J.; Polásek, M. J. Am. Chem. Soc. 1995, 117, 792.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 792
-
-
Hobza, P.1
Sponer, J.2
Polásek, M.3
-
31
-
-
33748621478
-
-
(f) Sponer, J.; Leszcyznski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 5590.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 5590
-
-
Sponer, J.1
Leszcyznski, J.2
Hobza, P.3
-
32
-
-
0029998770
-
-
(g) Sponer, J.; Leszcyznski, J.; Vetter, V.; Hobza, P. J. Biomol. Struct. Dyn. 1996, 13, 695.
-
(1996)
J. Biomol. Struct. Dyn.
, vol.13
, pp. 695
-
-
Sponer, J.1
Leszcyznski, J.2
Vetter, V.3
Hobza, P.4
-
33
-
-
0001225025
-
-
(h) Sponer, J. Leszcyznski, J.: Hobza, P. J. Comput. Chem. 1996, 17, 841.
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 841
-
-
Sponer, J.1
Leszcyznski, J.2
Hobza, P.3
-
35
-
-
4043135716
-
-
note
-
Insight II Computer Program, Biosym Technology, San Diego CA 1991. The preciseness of the fiber models obtained by Insight II was verified by comparison with those generated by NUCGEN-95 program developed by Kollman's research group at UCSF.
-
-
-
-
41
-
-
0001280462
-
-
(b) Tsuzuki, S.; Uchimaru, T.; Tanabe, K. J. Mol. Struct. (THEOCHEM) 1994, 307, 107.
-
(1994)
J. Mol. Struct. (THEOCHEM)
, vol.307
, pp. 107
-
-
Tsuzuki, S.1
Uchimaru, T.2
Tanabe, K.3
-
42
-
-
4043124570
-
-
note
-
The diffuse 6-31G(d) basis set is defined by using the standard basis set substituting the standard exponent of the d functions by 0.25.
-
-
-
-
43
-
-
0025728614
-
-
Pranata, J.; Wierschke, S. G.; Jorgensen, W. L. J. Am. Chem. Soc. 1991, 113, 2810.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 2810
-
-
Pranata, J.1
Wierschke, S.G.2
Jorgensen, W.L.3
-
44
-
-
0029011701
-
-
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.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179
-
-
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
Caldwell, J.W.9
Kollman, P.A.10
-
45
-
-
0004133516
-
-
Gaussian Inc. Pittsburgh, PA
-
Frisch, M. J.; Trucks, G. W.; Head-Gordon, M.; Gill, P. M. W.; Wong, M. W.; Foresman, J. B.; Johnson, B. G.; Schelgel, H. B.; Robb, M. A.; Replogle, E. S.; Gomperts, R.; Andres, J. L.; Raghavachari, K.; Binkey, J. S.; Gonzalen, C.; Martin, R. L.; Fox, D. J.; Defrees, D. J.; Baker, J.; Stewart, J. J. P., Pople, J. A. Gaussian 92 Gaussian Inc. Pittsburgh, PA, 1992.
-
(1992)
Gaussian 92
-
-
Frisch, M.J.1
Trucks, G.W.2
Head-Gordon, M.3
Gill, P.M.W.4
Wong, M.W.5
Foresman, J.B.6
Johnson, B.G.7
Schelgel, H.B.8
Robb, M.A.9
Replogle, E.S.10
Gomperts, R.11
Andres, J.L.12
Raghavachari, K.13
Binkey, J.S.14
Gonzalen, C.15
Martin, R.L.16
Fox, D.J.17
Defrees, D.J.18
Baker, J.19
Stewart, J.J.P.20
Pople, J.A.21
more..
-
46
-
-
0037721149
-
-
(a) Hobza, P.; Selzle, H. L.; Schlag, E. W. J. Phys. Chem. 1996, 100, 18790.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 18790
-
-
Hobza, P.1
Selzle, H.L.2
Schlag, E.W.3
-
47
-
-
0000213148
-
-
(b) Hobza, P.; Selzle, H. L.; Schlag, E. W. Chem. Rev. 1994, 94, 11767.
-
(1994)
Chem. Rev.
, vol.94
, pp. 11767
-
-
Hobza, P.1
Selzle, H.L.2
Schlag, E.W.3
-
49
-
-
33947485013
-
-
(a) Ts'o, P. O. P.; Melvin, I. S.; Olson, A. C. J. Am. Chem. Soc. 1963, 85, 1289.
-
(1963)
J. Am. Chem. Soc.
, vol.85
, pp. 1289
-
-
Ts'o, P.O.P.1
Melvin, I.S.2
Olson, A.C.3
-
53
-
-
0001465691
-
-
(e) Broom, A. D.; Schweizer, M. P.; Ts'o, P. O. P.; J. Am. Chem. Soc. 1967, 89, 3612.
-
(1967)
J. Am. Chem. Soc.
, vol.89
, pp. 3612
-
-
Broom, A.D.1
Schweizer, M.P.2
Ts'o, P.O.P.3
-
55
-
-
0015264832
-
-
(g) Powell, J. T.; Richards, E. G.; Gratzer, W. B., Biopolymers 1972, 11, 235.
-
(1972)
Biopolymers
, vol.11
, pp. 235
-
-
Powell, J.T.1
Richards, E.G.2
Gratzer, W.B.3
-
56
-
-
0015519015
-
-
(h) Guschlbauer, W.; Frick, I.; Holy, A. Eur. J. Biochem. 1972, 31, 1.
-
(1972)
Eur. J. Biochem.
, vol.31
, pp. 1
-
-
Guschlbauer, W.1
Frick, I.2
Holy, A.3
-
60
-
-
4043077640
-
-
(l) Lee, C.-H.; Ezra, F. S.; Kondo, N. S.; Sarma, R. H.; Danyluk, S. S. Biochemistry 1977, 16, 3627.
-
(1977)
Biochemistry
, vol.16
, pp. 3627
-
-
Lee, C.-H.1
Ezra, F.S.2
Kondo, N.S.3
Sarma, R.H.4
Danyluk, S.S.5
-
61
-
-
0017327646
-
-
(m) Ezra, F. S.; Lee, C.-H.; Kondo, N. S.; Danyluk, S. S.; Sarma, R. H. Biochemistry 1977, 16, 1977.
-
(1977)
Biochemistry
, vol.16
, pp. 1977
-
-
Ezra, F.S.1
Lee, C.-H.2
Kondo, N.S.3
Danyluk, S.S.4
Sarma, R.H.5
-
63
-
-
0017569069
-
-
(o) Suurkuusk, J.; Alvarez, J.; Freire, E.; Biltonen, R. Biopolymers 1977, 16, 2641.
-
(1977)
Biopolymers
, vol.16
, pp. 2641
-
-
Suurkuusk, J.1
Alvarez, J.2
Freire, E.3
Biltonen, R.4
-
64
-
-
0018788364
-
-
(p) Frechet, D.; Ehrlich, R.; Remy, P. Nucl. Acid Research 1979, 7, 1981.
-
(1979)
Acid Research
, vol.7
, pp. 1981
-
-
Frechet, D.1
Ehrlich, R.2
Nucl, R.P.3
-
65
-
-
0023667625
-
-
(q) Sowers, L. C.; Shaw, B. R.; Sedwick, W. D. Biochem. Biophys. Rese. Commun. 1987, 148, 790.
-
(1987)
Biochem. Biophys. Rese. Commun.
, vol.148
, pp. 790
-
-
Sowers, L.C.1
Shaw, B.R.2
Sedwick, W.D.3
-
66
-
-
0010814165
-
-
THEOCHEM
-
(r) Morcillo, J.; Gallego, E.; Peral, F. J. Mol. Struct. (THEOCHEM) 1987, 157, 353.
-
(1987)
J. Mol. Struct.
, vol.157
, pp. 353
-
-
Morcillo, J.1
Gallego, E.2
Peral, F.3
-
67
-
-
0042120232
-
-
THEOCHEM
-
(s) Iza, N.; Montera, J. L.; Morcillo, J. J. Mol. Struct. (THEOCHEM) 1988, 175, 19.
-
(1988)
J. Mol. Struct.
, vol.175
, pp. 19
-
-
Iza, N.1
Montera, J.L.2
Morcillo, J.3
-
68
-
-
4043159756
-
-
note
-
We have assumed in this paper that the MP2-HF difference is due only to dispersion interactions. This is an obvious simplification, but it is useful for discussion.
-
-
-
-
69
-
-
84986512474
-
-
(a) Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S. Karplus, M. J. Comput. Chem., 1983, 4, 187.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
70
-
-
6344260593
-
-
(b) MacKerell, A. D.; Wiórkiewicz-Kuczera, J.; Karplus, M. J. Am. Chem.Soc. 1995, 117, 11946.
-
(1995)
J. Am. Chem.Soc.
, vol.117
, pp. 11946
-
-
MacKerell, A.D.1
Wiórkiewicz-Kuczera, J.2
Karplus, M.3
-
71
-
-
4043154062
-
-
note
-
Overestimation of stacking stability in classical calculations might be smaller than that deduced from inspection of Figure 3. This is due to die tendency of MP2/6-31G(d) calculations to underestimate dispersion interactions.
-
-
-
-
72
-
-
0023494886
-
-
Coll, M.; Frederick, C. A.; Wang, A. H. J.; Rich, A. J. Proc. Natl. Acad. Sci. U.S.A., 1987, 84, 8385.
-
(1987)
Proc. Natl. Acad. Sci. U.S.A.
, vol.84
, pp. 8385
-
-
Coll, M.1
Frederick, C.A.2
Wang, A.H.J.3
Rich, A.J.4
-
73
-
-
0021103971
-
-
(a) Shakked, Z.; Rabinovich D.; Kennard, O.; Cruse, W. B.; Salisbury, S. A.; Viswamitra, M. A. J. Mol. Biol. 1983, 166, 183.
-
(1983)
J. Mol. Biol.
, vol.166
, pp. 183
-
-
Shakked, Z.1
Rabinovich, D.2
Kennard, O.3
Cruse, W.B.4
Salisbury, S.A.5
Viswamitra, M.A.6
-
74
-
-
0022508089
-
-
(b) McCall, M.; Brown, T.; Hunter, W. N.; Kennard, O. Nature 1986, 322, 661.
-
(1986)
Nature
, vol.322
, pp. 661
-
-
McCall, M.1
Brown, T.2
Hunter, W.N.3
Kennard, O.4
-
75
-
-
0024297080
-
-
(c) Lauble, H.; Frank, R.; Blocker, H.; Heinemann, U. Nucleic Acid Research 1988, 16, 7799.
-
(1988)
Nucleic Acid Research
, vol.16
, pp. 7799
-
-
Lauble, H.1
Frank, R.2
Blocker, H.3
Heinemann, U.4
-
76
-
-
0024595890
-
-
(d) Hunter, W. N.; D'Estaintot, B. L.; Kennard, O. Biochemistry 1989, 28, 2444.
-
(1989)
Biochemistry
, vol.28
, pp. 2444
-
-
Hunter, W.N.1
D'Estaintot, B.L.2
Kennard, O.3
-
78
-
-
0025335983
-
-
(f) Eisenstein, M.; Frolow, F.; Shakked, Z.; Rabinovich, D. Nucleic Acids Research 1990, 18, 3185.
-
(1990)
Nucleic Acids Research
, vol.18
, pp. 3185
-
-
Eisenstein, M.1
Frolow, F.2
Shakked, Z.3
Rabinovich, D.4
-
79
-
-
4043132965
-
-
(g) Jain, S.; Zon, G.: Sundaralingam, M. Biochemistry 1991, 30, 3576.
-
(1991)
Biochemistry
, vol.30
, pp. 3576
-
-
Jain, S.1
Zon, G.2
Sundaralingam, M.3
-
80
-
-
0008242360
-
-
(h) Cervi, A.; Lagnlois D'Estaintot, B.; Hunter, W. N. Acta Crystallogr., Sect. B.: Struct. Sci. 1992, 48, 714.
-
(1992)
Acta Crystallogr., Sect. B.: Struct. Sci.
, vol.48
, pp. 714
-
-
Cervi, A.1
Lagnlois D'Estaintot, B.2
Hunter, W.N.3
-
81
-
-
0026801023
-
-
(i) Bingman, C. A., Zon, G., Sundaralingam, M. J. Mol. Biol. 1992, 227, 738.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 738
-
-
Bingman, C.A.1
Zon, G.2
Sundaralingam, M.3
-
82
-
-
0027096732
-
-
(j) Bingman, C.; Jain, S.; Zong, G.; Sundaralingam, M. Nucleic Acids Research 1992, 20, 6637.
-
(1992)
Nucleic Acids Research
, vol.20
, pp. 6637
-
-
Bingman, C.1
Jain, S.2
Zong, G.3
Sundaralingam, M.4
-
83
-
-
0019558179
-
-
(a) Drew, H. R.; Wing, R. M.; Takano, T.; Broka, C.; Tanaka, S.; Itakura, K.; Dickerson, R. E. Prof. Natl Acad. Sci. U.S.A. 1981, 78, 2179.
-
(1981)
Prof. Natl Acad. Sci. U.S.A.
, vol.78
, pp. 2179
-
-
Drew, H.R.1
Wing, R.M.2
Takano, T.3
Broka, C.4
Tanaka, S.5
Itakura, K.6
Dickerson, R.E.7
-
84
-
-
0011205264
-
-
(b) Yoon, C.; Prive G. G.; Goodsell, D. S.; Dickerson R. E. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 6332.
-
(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, pp. 6332
-
-
Yoon, C.1
Prive, G.G.2
Goodsell, D.S.3
Dickerson, R.E.4
-
85
-
-
0025787463
-
-
(c) Narayama, N.; Genel, S. L.; Russu, I. M.; Berman, H. M. Biochemistry 1991, 30, 4449.
-
(1991)
Biochemistry
, vol.30
, pp. 4449
-
-
Narayama, N.1
Genel, S.L.2
Russu, I.M.3
Berman, H.M.4
-
86
-
-
0025816853
-
-
(d) Grzeskowiak, K.; Yanagi, K.; Prive, G. G.; Dickerson R. E.; J. Biol. Chem. 1991, 266, 8861.
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 8861
-
-
Grzeskowiak, K.1
Yanagi, K.2
Prive, G.G.3
Dickerson, R.E.4
-
87
-
-
0026624859
-
-
(e) Quintana, J. R.; Grzeskowiak, K.; Yanagi, K.; Dickerson, R. E. J. Mol. Biol. 1992, 225, 379.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 379
-
-
Quintana, J.R.1
Grzeskowiak, K.2
Yanagi, K.3
Dickerson, R.E.4
-
88
-
-
0026649309
-
-
(f) Yuan, H.; Quintana, J.; Dickerson, R. E. Biochemistry 1992, 31, 8009.
-
(1992)
Biochemistry
, vol.31
, pp. 8009
-
-
Yuan, H.1
Quintana, J.2
Dickerson, R.E.3
-
89
-
-
0026461079
-
-
(g) Edwards, K. J.; Brown, D. G.; Spink, N.; Skelly, J. V.; Neidle, S. J. Mol. Biol. 1992, 226, 1161.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 1161
-
-
Edwards, K.J.1
Brown, D.G.2
Spink, N.3
Skelly, J.V.4
Neidle, S.5
-
90
-
-
0027536101
-
-
(h) Goodsell, D. S.; Kopka, M. L.; Cascio, D.; Dickerson, R. E. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 2930.
-
(1993)
Proc. Natl. Acad. Sci. U.S.A.
, vol.90
, pp. 2930
-
-
Goodsell, D.S.1
Kopka, M.L.2
Cascio, D.3
Dickerson, R.E.4
-
92
-
-
0028225644
-
-
(j) Goodsell, D. S.; Kaczor-Grzeskowiak, M.; Dickerson, R. E. J. Mol. Biol. 1994, 239, 79.
-
(1994)
J. Mol. Biol.
, vol.239
, pp. 79
-
-
Goodsell, D.S.1
Kaczor-Grzeskowiak, M.2
Dickerson, R.E.3
|