-
1
-
-
0034708334
-
Structure and function of the hairpin ribozyme
-
Fedor, M. J. Structure and function of the hairpin ribozyme. J. Mol. Biol. 2000, 297, 269-291.
-
(2000)
J. Mol. Biol
, vol.297
, pp. 269-291
-
-
Fedor, M.J.1
-
2
-
-
0036753229
-
Two Decades of RNA Catalysis
-
DeRose, V. J. Two Decades of RNA Catalysis. Chem. Biol. 2002, 9, 961-969.
-
(2002)
Chem. Biol
, vol.9
, pp. 961-969
-
-
DeRose, V.J.1
-
3
-
-
0035020626
-
The hammerhead cleavage reaction in monovalent cations
-
Curtis, E. A.; Bartel, D. P. The hammerhead cleavage reaction in monovalent cations. RNA 2001, 7, 546-552.
-
(2001)
RNA
, vol.7
, pp. 546-552
-
-
Curtis, E.A.1
Bartel, D.P.2
-
4
-
-
0035001461
-
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations
-
O'Rear, J. L.; Wang, S.; Feig, A. L.; Beigelman, L.; Uhlenbeck, O. C.; Herschlag, D. Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA 2001, 7, 537-545.
-
(2001)
RNA
, vol.7
, pp. 537-545
-
-
O'Rear, J.L.1
Wang, S.2
Feig, A.L.3
Beigelman, L.4
Uhlenbeck, O.C.5
Herschlag, D.6
-
5
-
-
0035833978
-
Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism
-
Nakano, S.; Proctor, D. J.; Bevilacqua, P. C. Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry 2001, 40, 12022-12038.
-
(2001)
Biochemistry
, vol.40
, pp. 12022-12038
-
-
Nakano, S.1
Proctor, D.J.2
Bevilacqua, P.C.3
-
6
-
-
0037418547
-
Mechanistic considerations for general acid-base catalysis by RNA: Revisiting the mechanism of the hairpin ribozyme
-
Bevilacqua, P. C. Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme. Biochemistry 2003, 42, 2259-2265.
-
(2003)
Biochemistry
, vol.42
, pp. 2259-2265
-
-
Bevilacqua, P.C.1
-
7
-
-
0037111875
-
Transition state stabilization by a catalytic RNA
-
Rupert, P. B.; Massey, A. P.; Sigurdsson, S. Th.; Ferre-D'Amare, A. R. Transition state stabilization by a catalytic RNA. Science 2002, 298, 1421-1424.
-
(2002)
Science
, vol.298
, pp. 1421-1424
-
-
Rupert, P.B.1
Massey, A.P.2
Sigurdsson, S.T.3
Ferre-D'Amare, A.R.4
-
8
-
-
2942577491
-
Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue
-
Kuzmin, Y. I.; Da Costa, C. P.; Fedor, M. J. Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue. J. Mol. Biol. 2004, 340, 233-251.
-
(2004)
J. Mol. Biol
, vol.340
, pp. 233-251
-
-
Kuzmin, Y.I.1
Da Costa, C.P.2
Fedor, M.J.3
-
9
-
-
20344405966
-
Role of an active site adenine in hairpin ribozyme catalysis
-
Kuzmin, Y. I.; Da Costa, C. P.; Cottrell, J. W.; Fedor, M. J. Role of an active site adenine in hairpin ribozyme catalysis. J. Mol. Biol. 2005, 349, 989-1010.
-
(2005)
J. Mol. Biol
, vol.349
, pp. 989-1010
-
-
Kuzmin, Y.I.1
Da Costa, C.P.2
Cottrell, J.W.3
Fedor, M.J.4
-
10
-
-
0034712097
-
General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
-
Nakano, S.; Chadalavada, D. M.; Bevilacqua, P. C. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 2000, 287, 1493-1497.
-
(2000)
Science
, vol.287
, pp. 1493-1497
-
-
Nakano, S.1
Chadalavada, D.M.2
Bevilacqua, P.C.3
-
11
-
-
0035997396
-
Catalytic strategies of the hepatitis delta virus ribozymes
-
Shih, I.; Been, M. D. Catalytic strategies of the hepatitis delta virus ribozymes. Annu. Rev. Biochem. 2002, 71, 887-917.
-
(2002)
Annu. Rev. Biochem
, vol.71
, pp. 887-917
-
-
Shih, I.1
Been, M.D.2
-
12
-
-
0001067597
-
Force field design for metalloproteins
-
Hoops, S. C.; Anderson, K. W.; Merz, K. M., Jr. Force field design for metalloproteins. J. Am. Chem. Soc. 1991, 113, 8262-8270.
-
(1991)
J. Am. Chem. Soc
, vol.113
, pp. 8262-8270
-
-
Hoops, S.C.1
Anderson, K.W.2
Merz Jr., K.M.3
-
13
-
-
0000730887
-
Application of the RESP methodology in the parameterization of organic solvents
-
Fox, T.; Kollman, P. A. Application of the RESP methodology in the parameterization of organic solvents. J. Phys. Chem. B 1998, 102, 8070-8079.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 8070-8079
-
-
Fox, T.1
Kollman, P.A.2
-
14
-
-
0029011701
-
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
-
-
-
15
-
-
3042524904
-
-
Bayly, C. A.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A well behaved elestrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 1993, 97, 10269-10280.
-
Bayly, C. A.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A well behaved elestrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 1993, 97, 10269-10280.
-
-
-
-
16
-
-
23444454552
-
-
Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26, 1668-1688.
-
Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26, 1668-1688.
-
-
-
-
17
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
18
-
-
1242269406
-
Molecular dynamics simulations of DNA curvature and flexibility
-
Beveridge, D. L.; Dixit, S. B.; Barreiro, G.; Thayer, K. M. Molecular dynamics simulations of DNA curvature and flexibility. Biopolymers 2004, 73, 380-403.
-
(2004)
Biopolymers
, vol.73
, pp. 380-403
-
-
Beveridge, D.L.1
Dixit, S.B.2
Barreiro, G.3
Thayer, K.M.4
-
19
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684-3690.
-
(1984)
J. Chem. Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
20
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.C.3
-
21
-
-
0029115487
-
Zinc binding in proteins and solution: A simple but accurate nonbonded representation
-
Stote, R. H.; Karplus, M. Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins 1995, 23, 12-31.
-
(1995)
Proteins
, vol.23
, pp. 12-31
-
-
Stote, R.H.1
Karplus, M.2
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