-
1
-
-
0029071510
-
The molecular biology of hepatitis delta virus
-
Lai M.M. The molecular biology of hepatitis delta virus. Annu. Rev. Biochem. 1995, 64:259-286.
-
(1995)
Annu. Rev. Biochem.
, vol.64
, pp. 259-286
-
-
Lai, M.M.1
-
2
-
-
0032497521
-
Crystal structure of a hepatitis delta virus ribozyme
-
Ferre-D'Amare A.R., Zhou K., Doudna J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 1998, 395:567-574.
-
(1998)
Nature
, vol.395
, pp. 567-574
-
-
Ferre-D'Amare, A.R.1
Zhou, K.2
Doudna, J.A.3
-
3
-
-
0034695419
-
Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module
-
Ferre-D'Amare A.R., Doudna J.A. Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module. J. Mol. Biol. 2000, 295:541-556.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 541-556
-
-
Ferre-D'Amare, A.R.1
Doudna, J.A.2
-
4
-
-
2442641641
-
A conformational switch controls hepatitis delta virus ribozyme catalysis
-
Ke A., Zhou K., Ding F., Cate J.H., Doudna J.A. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 2004, 429:201-205.
-
(2004)
Nature
, vol.429
, pp. 201-205
-
-
Ke, A.1
Zhou, K.2
Ding, F.3
Cate, J.H.4
Doudna, J.A.5
-
5
-
-
33847691104
-
Structural roles of monovalent cations in the HDV ribozyme
-
Ke A., Ding F., Batchelor J.D., Doudna J.A. Structural roles of monovalent cations in the HDV ribozyme. Structure 2007, 15:281-287.
-
(2007)
Structure
, vol.15
, pp. 281-287
-
-
Ke, A.1
Ding, F.2
Batchelor, J.D.3
Doudna, J.A.4
-
7
-
-
0033053643
-
A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes
-
Wadkins T.S., Perrotta A.T., Ferre-D'Amare A.R., Doudna J.A., Been M.D. A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. RNA 1999, 5:720-727.
-
(1999)
RNA
, vol.5
, pp. 720-727
-
-
Wadkins, T.S.1
Perrotta, A.T.2
Ferre-D'Amare, A.R.3
Doudna, J.A.4
Been, M.D.5
-
8
-
-
33749034196
-
A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene
-
Salehi-Ashtiani K., Luptak A., Litovchick A., Szostak J.W. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science 2006, 313:1788-1792.
-
(2006)
Science
, vol.313
, pp. 1788-1792
-
-
Salehi-Ashtiani, K.1
Luptak, A.2
Litovchick, A.3
Szostak, J.W.4
-
9
-
-
72449145407
-
Widespread occurrence of self-cleaving ribozymes
-
Webb C.H.T., Riccitelli N.J., Ruminski D.J., Lupták A. Widespread occurrence of self-cleaving ribozymes. Science 2009, 326:953.
-
(2009)
Science
, vol.326
, pp. 953
-
-
Webb, C.H.T.1
Riccitelli, N.J.2
Ruminski, D.J.3
Lupták, A.4
-
10
-
-
24644454458
-
General acid catalysis by the hepatitis delta virus ribozyme
-
Das S.R., Piccirilli J.A. General acid catalysis by the hepatitis delta virus ribozyme. Nat. Chem. Biol. 2005, 1:45-52.
-
(2005)
Nat. Chem. Biol.
, vol.1
, pp. 45-52
-
-
Das, S.R.1
Piccirilli, J.A.2
-
11
-
-
55549085243
-
Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid
-
Cerrone-Szakal A.L., Siegfried N.A., Bevilacqua P.C. Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid. J. Am. Chem. Soc. 2008, 130:14504-14520.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 14504-14520
-
-
Cerrone-Szakal, A.L.1
Siegfried, N.A.2
Bevilacqua, P.C.3
-
12
-
-
0026597714
-
Deletion of internal sequence on the HDV-ribozyme: elucidation of functionally important single-stranded loop regions
-
Suh Y.A., Kumar P.K., Nishikawa F., Kayano E., Nakai S., Odai O., et al. Deletion of internal sequence on the HDV-ribozyme: elucidation of functionally important single-stranded loop regions. Nucleic Acids Res. 1992, 20:747-753.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 747-753
-
-
Suh, Y.A.1
Kumar, P.K.2
Nishikawa, F.3
Kayano, E.4
Nakai, S.5
Odai, O.6
-
13
-
-
0030803589
-
Self-cleaving ribozymes of hepatitis delta virus RNA
-
Been M.D., Wickham G.S. Self-cleaving ribozymes of hepatitis delta virus RNA. Eur. J. Biochem. 1997, 247:741-753.
-
(1997)
Eur. J. Biochem.
, vol.247
, pp. 741-753
-
-
Been, M.D.1
Wickham, G.S.2
-
14
-
-
36248964100
-
Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions
-
Chadalavada D.M., Cerrone-Szakal A.L., Bevilacqua P.C. Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions. RNA 2007, 13:2189-2201.
-
(2007)
RNA
, vol.13
, pp. 2189-2201
-
-
Chadalavada, D.M.1
Cerrone-Szakal, A.L.2
Bevilacqua, P.C.3
-
15
-
-
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
-
16
-
-
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
-
17
-
-
33947356675
-
Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons
-
Nakano S., Bevilacqua P.C. Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons. Biochemistry 2007, 46:3001-3012.
-
(2007)
Biochemistry
, vol.46
, pp. 3001-3012
-
-
Nakano, S.1
Bevilacqua, P.C.2
-
18
-
-
0035793217
-
A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion
-
Wadkins T.S., Shih I., Perrotta A.T., Been M.D. A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion. J. Mol. Biol. 2001, 305:1045-1055.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 1045-1055
-
-
Wadkins, T.S.1
Shih, I.2
Perrotta, A.T.3
Been, M.D.4
-
19
-
-
0036385783
-
Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot
-
Nixon P.L., Rangan A., Kim Y.G., Rich A., Hoffman D.W., Hennig M., Giedroc D.P. Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot. J. Mol. Biol. 2002, 322:621-633.
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 621-633
-
-
Nixon, P.L.1
Rangan, A.2
Kim, Y.G.3
Rich, A.4
Hoffman, D.W.5
Hennig, M.6
Giedroc, D.P.7
-
20
-
-
33749015209
-
Molecular biology. Versatility of self-cleaving ribozymes
-
Been M.D. Molecular biology. Versatility of self-cleaving ribozymes. Science 2006, 313:1745-1747.
-
(2006)
Science
, vol.313
, pp. 1745-1747
-
-
Been, M.D.1
-
22
-
-
0347763707
-
Catalytic roles for proton transfer and protonation in ribozymes
-
Bevilacqua P.C., Brown T.S., Nakano S., Yajima R. Catalytic roles for proton transfer and protonation in ribozymes. Biopolymers 2004, 73:90-109.
-
(2004)
Biopolymers
, vol.73
, pp. 90-109
-
-
Bevilacqua, P.C.1
Brown, T.S.2
Nakano, S.3
Yajima, R.4
-
24
-
-
70349272668
-
Catalytic mechanism of the HDV ribozyme
-
RSC Publishing, Cambridge, UK, D.M. Lilley, F. Eckstein (Eds.)
-
Koo S., Novak T., Piccirilli J.A. Catalytic mechanism of the HDV ribozyme. Ribozymes and RNA Catalysis 2008, 92-122. RSC Publishing, Cambridge, UK. D.M. Lilley, F. Eckstein (Eds.).
-
(2008)
Ribozymes and RNA Catalysis
, pp. 92-122
-
-
Koo, S.1
Novak, T.2
Piccirilli, J.A.3
-
25
-
-
23444456517
-
Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations
-
Krasovska M.V., Sefcikova J., Spackova N., Sponer J., Walter N.G. Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J. Mol. Biol. 2005, 351:731-748.
-
(2005)
J. Mol. Biol.
, vol.351
, pp. 731-748
-
-
Krasovska, M.V.1
Sefcikova, J.2
Spackova, N.3
Sponer, J.4
Walter, N.G.5
-
26
-
-
77955258795
-
A 1.9 Å crystal structure of the HDV ribozyme pre-cleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester bond cleavage
-
Chen J., Yajima R., Chadalavada D., Chase E., Bevilacqua P.C., Golden B.L A 1.9 Å crystal structure of the HDV ribozyme pre-cleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester bond cleavage. Biochemistry 2010, 49:6508-6518.
-
(2010)
Biochemistry
, vol.49
, pp. 6508-6518
-
-
Chen, J.1
Yajima, R.2
Chadalavada, D.3
Chase, E.4
Bevilacqua, P.C.5
Golden, B.L.6
-
27
-
-
0027436419
-
Identification of important bases in a single-stranded region (SSrC) of the hepatitis delta (delta) virus ribozyme
-
Kawakami J., Kumar P.K., Suh Y.A., Nishikawa F., Kawakami K., Taira K., et al. Identification of important bases in a single-stranded region (SSrC) of the hepatitis delta (delta) virus ribozyme. Eur. J. Biochem. 1993, 217:29-36.
-
(1993)
Eur. J. Biochem.
, vol.217
, pp. 29-36
-
-
Kawakami, J.1
Kumar, P.K.2
Suh, Y.A.3
Nishikawa, F.4
Kawakami, K.5
Taira, K.6
-
29
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory analysis
-
Lindahl E., Hess B., van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7:306-317.
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
30
-
-
0002161378
-
DLPROTEIN: a molecular dynamics package to simulate biomolecules
-
Supercomputing Group, CINECA, Bologna, Italy, M. Voli (Ed.)
-
Melchionna S., Luise A., Venturoli M., Cozzini S. DLPROTEIN: a molecular dynamics package to simulate biomolecules. Science and Supercomputing at CINECA-1997 Report 1998, 496-505. Supercomputing Group, CINECA, Bologna, Italy. M. Voli (Ed.).
-
(1998)
Science and Supercomputing at CINECA-1997 Report
, pp. 496-505
-
-
Melchionna, S.1
Luise, A.2
Venturoli, M.3
Cozzini, S.4
-
31
-
-
77956173654
-
-
Desmond Molecular Dynamics System, D.E. Shaw Research, New York .
-
Desmond Molecular Dynamics System, D. E. Shaw Research, New York (2008).
-
(2008)
-
-
-
32
-
-
34548283148
-
Scalable algorithms for molecular dynamics simulations on commodity clusters
-
The Association for Computing Machinery (ACM) Press, Tampa, Florida
-
Bowers K.J., Chow E., Xu H., Dror R.O., Eastwood M.P., Gregersen B.A., et al. Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the ACM/IEEE Conference on Supercomputing (SC06) 2006, The Association for Computing Machinery (ACM) Press, Tampa, Florida.
-
(2006)
Proceedings of the ACM/IEEE Conference on Supercomputing (SC06)
-
-
Bowers, K.J.1
Chow, E.2
Xu, H.3
Dror, R.O.4
Eastwood, M.P.5
Gregersen, B.A.6
-
33
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M.J., Ferguson D.M., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. 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.J.5
Ferguson, D.M.6
-
34
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules
-
Wang J.M., Cieplak P., Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules. J. Comp. Chem. 2000, 21:1049-1074.
-
(2000)
J. Comp. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.M.1
Cieplak, P.2
Kollman, P.A.3
-
35
-
-
77956171557
-
-
Automatic and highly reproducible RESP and ESP charge derivation: application to the development of programs RED and X RED. 227th ACS National Meeting, Anaheim, CA. March 28-April 1.
-
Pigache, A., Cieplak, P. & Dupradeau, F. Y. Automatic and highly reproducible RESP and ESP charge derivation: application to the development of programs RED and X RED. 227th ACS National Meeting, Anaheim, CA. March 28-April 1, 2004.
-
(2004)
-
-
Pigache, A.1
Cieplak, P.2
Dupradeau, F.Y.3
-
36
-
-
15744375697
-
-
Gaussian, Inc, Wallingford, CT
-
Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., et al. Gaussian03 (Revision C.02) 2003, Gaussian, Inc, Wallingford, CT.
-
(2003)
Gaussian03 (Revision C.02)
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
-
37
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: the RESP model
-
Bayly C.I., Cieplak P., Cornell W.D., Kollman P.A. A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: the RESP model. J. Phys. Chem. 1993, 97:10269-10280.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
38
-
-
84986516411
-
Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins
-
Cieplak P., Cornell W.D., Bayly C., Kollman P.A. Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins. J. Comput. Chem. 1995, 16:1357-1377.
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1357-1377
-
-
Cieplak, P.1
Cornell, W.D.2
Bayly, C.3
Kollman, P.A.4
-
39
-
-
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
-
40
-
-
33846823909
-
Particle mesh Ewald: an N log (N) method for Ewald sums in large systems
-
Darden T., York D., Pedersen L. Particle mesh Ewald: an N log (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98:10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
41
-
-
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.J.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.J.C.3
-
42
-
-
84943502952
-
A molecular dynamics method for simulations in the canonical ensemble
-
Nosé S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 1984, 52:255-268.
-
(1984)
Mol. Phys.
, vol.52
, pp. 255-268
-
-
Nosé, S.1
-
43
-
-
0001538909
-
Canonical dynamics: equilibrium phase-space distributions
-
Hoover W.G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 1985, 31:1695-1697.
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
|