-
1
-
-
0017366365
-
-
Holbrook, S. R.; Sussman, J. L.; Warrant, R. W.; Church, G. M.; Kim, S. H. Nucleic Acids Res. 1977, 4, 2811.
-
(1977)
Nucleic Acids Res.
, vol.4
, pp. 2811
-
-
Holbrook, S.R.1
Sussman, J.L.2
Warrant, R.W.3
Church, G.M.4
Kim, S.H.5
-
2
-
-
0030476765
-
-
(a) Scott, W. G.; Murray, J. B.; Arnold, J. R. P.; Stoddard, B. L.; Klug, A. Science 1996, 274, 2065.
-
(1996)
Science
, vol.274
, pp. 2065
-
-
Scott, W.G.1
Murray, J.B.2
Arnold, J.R.P.3
Stoddard, B.L.4
Klug, A.5
-
4
-
-
0030929889
-
-
Cate, J. H.; Hanna, R. L.; Doudna, J. A. Nature Struct. Biol. 1997, 4, 553.
-
(1997)
Nature Struct. Biol.
, vol.4
, pp. 553
-
-
Cate, J.H.1
Hanna, R.L.2
Doudna, J.A.3
-
7
-
-
0036263869
-
-
(b) Huppler, A.; Niskstad, L. J.; Allman, A. M.; Brow, D. A.; Butcher, S. E. Nature Struct. Biol. 2002, 9, 431.
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 431
-
-
Huppler, A.1
Niskstad, L.J.2
Allman, A.M.3
Brow, D.A.4
Butcher, S.E.5
-
8
-
-
0037007108
-
-
Egli, M.; Minasov, G.; Su, L.; Rich, A. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 4302.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 4302
-
-
Egli, M.1
Minasov, G.2
Su, L.3
Rich, A.4
-
9
-
-
0030856333
-
-
(a) Correll, C. C.; Freeborn, B.; Moore, P. B.; Steitz, T. A. Cell 1997, 91, 705.
-
(1997)
Cell
, vol.91
, pp. 705
-
-
Correll, C.C.1
Freeborn, B.2
Moore, P.B.3
Steitz, T.A.4
-
17
-
-
0024463671
-
-
(a) Bernues, J.; Beltran, R.; Casasnovas, J. M.; Azorin, F. EMBO J. 1989, 8, 2087.
-
(1989)
EMBO J.
, vol.8
, pp. 2087
-
-
Bernues, J.1
Beltran, R.2
Casasnovas, J.M.3
Azorin, F.4
-
18
-
-
0027302170
-
-
(b) Cherney, D. I.; Malkov, V. A.; Volodin, A. A.; Frank-Kamenetskii, M. D. J. Mol. Biol. 1993, 230, 379.
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 379
-
-
Cherney, D.I.1
Malkov, V.A.2
Volodin, A.A.3
Frank-Kamenetskii, M.D.4
-
20
-
-
0034666413
-
-
Khomyakova, E. B.; Gousset, H.; Liquier, J.; Huynh-Dinh, T.; Gouyette, C.; Takahashi, M.; Florentiev, V. L.; Taillandier, E. Nucleic Acids Res. 2000, 18, 3511.
-
(2000)
Nucleic Acids Res.
, vol.18
, pp. 3511
-
-
Khomyakova, E.B.1
Gousset, H.2
Liquier, J.3
Huynh-Dinh, T.4
Gouyette, C.5
Takahashi, M.6
Florentiev, V.L.7
Taillandier, E.8
-
21
-
-
0042234575
-
-
Bernues, J.; Beltran, R.; Casasnovas; J. M.; Azorin, F. Nucleic Acids Res. 1991, 19, 1633.
-
(1991)
Nucleic Acids Res.
, vol.19
, pp. 1633
-
-
Bernues, J.1
Beltran, R.2
Casasnovas, J.M.3
Azorin, F.4
-
22
-
-
0032497951
-
-
McFail-Isom, L.; Shui, X. Q.; Williams, L. D. Biochemistry 1998, 37, 17105.
-
(1998)
Biochemistry
, vol.37
, pp. 17105
-
-
McFail-Isom, L.1
Shui, X.Q.2
Williams, L.D.3
-
23
-
-
0042735594
-
-
(a) Sponer, J.; Sponer, J. E.; Leszczynski, J. J. Biomol. Struct. Dyn. 2000, 17, 108.
-
(2000)
J. Biomol. Struct. Dyn.
, vol.17
, pp. 108
-
-
Sponer, J.1
Sponer, J.E.2
Leszczynski, J.3
-
24
-
-
0037188003
-
-
(b) Petrov, A. S.; Lamm, G.; Pack, G. R. J. Phys. Chem. B 2002, 106, 3294.
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 3294
-
-
Petrov, A.S.1
Lamm, G.2
Pack, G.R.3
-
27
-
-
0035834495
-
-
(a) Csaszar, K.; Spacková, N.; Stefl, R.; Sponer, J.; Leontis, N. B. J. Mol. Biol. 2001, 313, 1073.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 1073
-
-
Csaszar, K.1
Spacková, N.2
Stefl, R.3
Sponer, J.4
Leontis, N.B.5
-
28
-
-
0041734195
-
-
in press
-
(b) Reblova, K.; Spackova, N.; Stefl, R.; Csaszar, K.; Koca, J.; Leontis, N. B.; Sponer, J. Biophys. J. 2003, 84, in press.
-
(2003)
Biophys. J.
, vol.84
-
-
Reblova, K.1
Spackova, N.2
Stefl, R.3
Csaszar, K.4
Koca, J.5
Leontis, N.B.6
Sponer, J.7
-
29
-
-
0040164390
-
-
(a) Spackova, N.; Berger, I.; Sponer, J. J. Am. Chem. Soc. 1999, 121, 5519.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 5519
-
-
Spackova, N.1
Berger, I.2
Sponer, J.3
-
30
-
-
0034836422
-
-
(b) Spackova, N.; Berger, I.; Sponer, J. J. Am. Chem. Soc. 2001, 123, 3295.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 3295
-
-
Spackova, N.1
Berger, I.2
Sponer, J.3
-
32
-
-
0030849184
-
-
Hermann, T.; Auffinger, P.; Scott, W. G.; Westhof, E. Nucleic Acids Res. 1997, 25, 3421.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3421
-
-
Hermann, T.1
Auffinger, P.2
Scott, W.G.3
Westhof, E.4
-
36
-
-
0345631645
-
-
(c) Sponer, J.; Burda, J. V.; Sabat, M.; Leszczynski, J.; Hobza, P. J. Phys. Chem. A 1998, 102, 5951.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 5951
-
-
Sponer, J.1
Burda, J.V.2
Sabat, M.3
Leszczynski, J.4
Hobza, P.5
-
37
-
-
0036290781
-
-
Haider, S.; Parkinson, G. N.; Neidle, S. J. Mol. Biol. 2002, 320, 189.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 189
-
-
Haider, S.1
Parkinson, G.N.2
Neidle, S.3
-
40
-
-
84987055122
-
-
(b) Gresh, N.; Claverie, P.; Pullman, A. Int. J. Quantum Chem. 1986, 29, 101.
-
(1986)
Int. J. Quantum Chem.
, vol.29
, pp. 101
-
-
Gresh, N.1
Claverie, P.2
Pullman, A.3
-
43
-
-
0032054016
-
-
(a) Garmer, D.; Gresh, N.; Roques, B. P. Proteins 1998, 31, 42.
-
(1998)
Proteins
, vol.31
, pp. 42
-
-
Garmer, D.1
Gresh, N.2
Roques, B.P.3
-
44
-
-
0000111275
-
-
(b) Tiraboschi, G.; Gresh, N.; Giessner-Prettre, C.; Pedersen, L. G.; Deerfield, D. W. J. Comput. Chem. 2000, 21, 1011.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1011
-
-
Tiraboschi, G.1
Gresh, N.2
Giessner-Prettre, C.3
Pedersen, L.G.4
Deerfield, D.W.5
-
46
-
-
33748639068
-
-
(b) Masella, M.; Gresh, N.; Flament, J. P. J. Chem. Soc., Faraday Trans. 1998, 94, 2745.
-
(1998)
J. Chem. Soc., Faraday Trans.
, vol.94
, pp. 2745
-
-
Masella, M.1
Gresh, N.2
Flament, J.P.3
-
47
-
-
0343442498
-
-
(c) Guo, H.; Gresh, N.; Roques, B. P.; Salahub, D. R. J. Phys. Chem. B 2000, 105. 9746.
-
(2000)
J. Phys. Chem. B
, vol.105
, pp. 9746
-
-
Guo, H.1
Gresh, N.2
Roques, B.P.3
Salahub, D.R.4
-
49
-
-
0036771627
-
-
(b) Antony, J.; Gresh, N.; Olsen, L.; Hemmingsen, L.; Schofield, C.; Bauer, R. J. Comput. Chem. 2002, 23. 1281.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1281
-
-
Antony, J.1
Gresh, N.2
Olsen, L.3
Hemmingsen, L.4
Schofield, C.5
Bauer, R.6
-
52
-
-
0034249870
-
-
Sponer, J.; Sabat, M.; Gorb, L.; Leszczynski, J.; Lippert, B.; Hobza, P. J. Phys. Chem. B 2000, 104, 7535.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 7535
-
-
Sponer, J.1
Sabat, M.2
Gorb, L.3
Leszczynski, J.4
Lippert, B.5
Hobza, P.6
-
55
-
-
0005376894
-
-
Langlet, J.; Claverie, P.; Caillet, J.; Pullman, A. J. Phys. Chem. 1988, 92, 1631.
-
(1988)
J. Phys. Chem.
, vol.92
, pp. 1631
-
-
Langlet, J.1
Claverie, P.2
Caillet, J.3
Pullman, A.4
-
56
-
-
0028849248
-
-
Langlet, J.; Gresh, N.; Giessner-Prettre, C. Biopolymers 1995, 36, 765.
-
(1995)
Biopolymers
, vol.36
, pp. 765
-
-
Langlet, J.1
Gresh, N.2
Giessner-Prettre, C.3
-
57
-
-
0000304948
-
-
Tannor, D. J.; Marten, B.; Murphy, R.; Friesner, R. A.; Sitkoff, D.; Nicholls, A.; Ringnalda, M.; Goddard, W. A., III; Honig, B. J. Am. Chem. Soc. 1994, 116, 11875.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 11875
-
-
Tannor, D.J.1
Marten, B.2
Murphy, R.3
Friesner, R.A.4
Sitkoff, D.5
Nicholls, A.6
Ringnalda, M.7
Goddard W.A. III8
Honig, B.9
-
62
-
-
0005744966
-
-
Stevens, W. J.; Basch, H.; Krauss, M. J. Chem. Phys. 1984, 81, 6026.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 6026
-
-
Stevens, W.J.1
Basch, H.2
Krauss, M.3
-
63
-
-
0003154550
-
-
(a) Rogalewicz, F.; Ohanessian, G.; Gresh, N. J. Comput. Chem. 2000, 21, 963.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 963
-
-
Rogalewicz, F.1
Ohanessian, G.2
Gresh, N.3
-
64
-
-
0035974487
-
-
(b) Tiraboschi, G.; Fournié-Zaluski, M. C.; Roques, B. P.; Gresh, N. J. Comput. Chem. 2001, 22, 1038.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 1038
-
-
Tiraboschi, G.1
Fournié-Zaluski, M.C.2
Roques, B.P.3
Gresh, N.4
-
66
-
-
45949117576
-
-
Evangelakis, G. A.; Rizos, J. P.; Lagaris, I. E.; Demetropoulos, I. N. Comput. Phys. Commun. 1987, 46, 401.
-
(1987)
Comput. Phys. Commun.
, vol.46
, pp. 401
-
-
Evangelakis, G.A.1
Rizos, J.P.2
Lagaris, I.E.3
Demetropoulos, I.N.4
-
68
-
-
0009687148
-
-
Cammi, R.; Hofmann, H.-F.; Tomasi, J. Theor. Chim. Acta 1989, 76, 297.
-
(1989)
Theor. Chim. Acta
, vol.76
, pp. 297
-
-
Cammi, R.1
Hofmann, H.-F.2
Tomasi, J.3
-
69
-
-
84986444438
-
-
Pople, J. A.; Binkley, J. S.; Seeger, R. Int. J. Quantum Chem. Symp. 1976, 10, 1.
-
(1976)
Int. J. Quantum Chem. Symp.
, vol.10
, pp. 1
-
-
Pople, J.A.1
Binkley, J.S.2
Seeger, R.3
-
70
-
-
84893169025
-
-
Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A., Jr. J. Comput. Chem. 1993, 14, 1347.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1347
-
-
Schmidt, M.W.1
Baldridge, K.K.2
Boatz, J.A.3
Elbert, S.T.4
Gordon, M.S.5
Jensen, J.H.6
Koseki, S.7
Matsunaga, N.8
Nguyen, K.A.9
Su, S.10
Windus, T.L.11
Dupuis, M.12
Montgomery J.A., Jr.13
-
71
-
-
0345491105
-
-
(a) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. 1988, B37, 785.
-
(1988)
Phys. Rev.
, vol.B37
, pp. 785
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
74
-
-
0004133516
-
-
Gaussian, Inc.: Pittsburgh, PA
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98, Revision A.6; Gaussian, Inc.: Pittsburgh, PA, 1998.
-
(1998)
Gaussian 98, Revision A.6
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Zakrzewski, V.G.7
Montgomery J.A., Jr.8
Stratmann, R.E.9
Burant, J.C.10
Dapprich, S.11
Millam, J.M.12
Daniels, A.D.13
Kudin, K.N.14
Strain, M.C.15
Farkas, O.16
Tomasi, J.17
Barone, V.18
Cossi, M.19
Cammi, R.20
Mennucci, B.21
Pomelli, C.22
Adamo, C.23
Clifford, S.24
Ochterski, J.25
Petersson, G.A.26
Ayala, P.Y.27
Cui, Q.28
Morokuma, K.29
Malick, D.K.30
Rabuck, A.D.31
Raghavachari, K.32
Foresman, J.B.33
Cioslowski, J.34
Ortiz, J.V.35
Stefanov, B.B.36
Liu, G.37
Liashenko, A.38
Piskorz, P.39
Komaromi, I.40
Gomperts, R.41
Martin, R.L.42
Fox, D.J.43
Keith, T.44
Al-Laham, M.A.45
Peng, C.Y.46
Nanayakkara, A.47
Gonzalez, C.48
Challacombe, M.49
Gill, P.M.W.50
Johnson, B.51
Chen, W.52
Wong, M.W.53
Andres, J.L.54
Gonzalez, C.55
Head-Gordon, M.56
Replogle, E.S.57
Pople, J.A.58
more..
-
75
-
-
0042234574
-
-
Jaguar 4.1, Schrodinger Inc., Portland, OR
-
Jaguar 4.1, Schrodinger Inc., Portland, OR, 2000.
-
-
-
-
76
-
-
36549103818
-
-
Hurley, M. M.; Pacios, L. F.; Christiansen, P. A.; Roos, R. B.; Ermler, W. C. J. Chem. Phys. 1986, 84, 6840.
-
(1986)
J. Chem. Phys.
, vol.84
, pp. 6840
-
-
Hurley, M.M.1
Pacios, L.F.2
Christiansen, P.A.3
Roos, R.B.4
Ermler, W.C.5
-
77
-
-
0042735592
-
-
note
-
Since for such comparisons we did not compute the intramolecular interactions between the methyl phosphate fragments, we used here the multipolar expansion of the whole molecule rather than those of its isolated fragments.
-
-
-
-
78
-
-
84987090062
-
-
Pullman, B.; Pullman, A.; Berthod, H. Int. J. Quantum Chem. Symp. 1978, 5, 79.
-
(1978)
Int. J. Quantum Chem. Symp.
, vol.5
, pp. 79
-
-
Pullman, B.1
Pullman, A.2
Berthod, H.3
-
79
-
-
0001683231
-
-
Tiraboschi, G.; Roques, B. P.; Gresh, N. J. Comput. Chem. 1999, 20, 1379.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1379
-
-
Tiraboschi, G.1
Roques, B.P.2
Gresh, N.3
-
80
-
-
0035960215
-
-
Dubois, C.; Archirel, P.; Boutin, A. J. Phys. Chem. B 2001, 105, 9363.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 9363
-
-
Dubois, C.1
Archirel, P.2
Boutin, A.3
-
83
-
-
84986461296
-
-
(b) Hobza, P.; Sponer, J.; Reschel, T. J. Comput. Chem. 1995, 16, 1315.
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1315
-
-
Hobza, P.1
Sponer, J.2
Reschel, T.3
-
84
-
-
0038398783
-
-
(c) Perez-Jorda, M. M.; san-Fabian, E.; Perez-Jimenez, A. J. J. Chem. Phys. 1999, 110, 1916.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 1916
-
-
Perez-Jorda, M.M.1
San-Fabian, E.2
Perez-Jimenez, A.J.3
-
85
-
-
0031250361
-
-
(d) Wesolowski, T. A.; Parisel, O.; Ellinger, Y.; Weber, J. J. Phys. Chem. A 1997, 101, 7818.
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 7818
-
-
Wesolowski, T.A.1
Parisel, O.2
Ellinger, Y.3
Weber, J.4
-
90
-
-
0001398008
-
-
(a) Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
91
-
-
0004195760
-
-
University of California, San Francisco
-
(b) Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E. III; Wang, J.; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Gohlke, H.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 7, University of California, San Francisco, 2002.
-
(2002)
AMBER 7
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham T.E. III4
Wang, J.5
Ross, W.S.6
Simmerling, C.L.7
Darden, T.A.8
Merz, K.M.9
Stanton, R.V.10
Cheng, A.L.11
Vincent, J.J.12
Crowley, M.13
Tsui, V.14
Gohlke, H.15
Radmer, R.J.16
Duan, Y.17
Pitera, J.18
Massova, I.19
Seibel, G.L.20
Singh, U.C.21
Weiner, P.K.22
Kollman, P.A.23
more..
-
94
-
-
0038463891
-
-
Foloppe, N.; Nilsson, L.; MacKerell, A. D. Jr. Biopolymers 2002, 61, 61.
-
(2002)
Biopolymers
, vol.61
, pp. 61
-
-
Foloppe, N.1
Nilsson, L.2
MacKerell A.D., Jr.3
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