-
1
-
-
29844453234
-
Topology of three-way junctions in folded RNAs
-
Lescoute,A. and Westhof,E. (2006) Topology of three-way junctions in folded RNAs. RNA, 12, 83-93.
-
(2006)
RNA
, vol.12
, pp. 83-93
-
-
Lescoute, A.1
Westhof, E.2
-
2
-
-
33847318371
-
Molecular dynamics simulations of RNA: an in silico single molecule approach
-
McDowell,S.E., Spackova,N., Sponer,J. and Walter,N.G. (2007) Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers, 85, 169-184.
-
(2007)
Biopolymers
, vol.85
, pp. 169-184
-
-
McDowell, S.E.1
Spackova, N.2
Sponer, J.3
Walter, N.G.4
-
4
-
-
34347404466
-
Nucleic acid solvation: from outside to insight
-
Auffinger,P. and Hashem,Y. (2007) Nucleic acid solvation: from outside to insight. Curr. Opin. Struct. Biol., 17, 325-333.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 325-333
-
-
Auffinger, P.1
Hashem, Y.2
-
5
-
-
2942547665
-
Simulation and modeling of nucleic acid structure, dynamics and interactions
-
Cheatham,T.E. (2004) Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol., 14, 360-367.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 360-367
-
-
Cheatham, T.E.1
-
6
-
-
70349270612
-
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM
-
Banas,P., Jurecka,P., Walter,N.G., Sponer,J. and Otyepka,M. (2009) Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods, 49, 202-216.
-
(2009)
Methods
, vol.49
, pp. 202-216
-
-
Banas, P.1
Jurecka, P.2
Walter, N.G.3
Sponer, J.4
Otyepka, M.5
-
7
-
-
75449112058
-
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in
-
Ditzler,M.A., Otyepka,M., Šponer,J. and Walter,N.G. (2010) Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc. Chem. Res., 43, 40-47.
-
(2010)
Acc. Chem. Res.
, vol.43
, pp. 40-47
-
-
Ditzler, M.A.1
Otyepka, M.2
Šponer, J.3
Walter, N.G.4
-
8
-
-
42949089487
-
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
-
Trabuco,L.G., Villa,E., Mitra,K., Frank,J. and Schulten,K. (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure, 16, 673-683.
-
(2008)
Structure
, vol.16
, pp. 673-683
-
-
Trabuco, L.G.1
Villa, E.2
Mitra, K.3
Frank, J.4
Schulten, K.5
-
9
-
-
69049108817
-
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
-
Villa,A., Wöhnert,J. and Stock,G. (2009) Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res., 37, 4774-4786.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4774-4786
-
-
Villa, A.1
Wöhnert, J.2
Stock, G.3
-
10
-
-
0346366808
-
Symmetric K+ and Mg2+ ion-binding sites in the 5 S rRNA loop E inferred from molecular dynamics simulations
-
Auffinger,P., Bielecki,L. and Westhof,E. (2004) Symmetric K+ and Mg2+ ion-binding sites in the 5 S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol., 335, 555-571.
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 555-571
-
-
Auffinger, P.1
Bielecki, L.2
Westhof, E.3
-
11
-
-
33746388359
-
Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations
-
Reblova,K., Lankas,F., Razga,F., Krasovska,M.V., Koca,J. and Sponer,J. (2006) Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers, 82, 504-520.
-
(2006)
Biopolymers
, vol.82
, pp. 504-520
-
-
Reblova, K.1
Lankas, F.2
Razga, F.3
Krasovska, M.V.4
Koca, J.5
Sponer, J.6
-
12
-
-
0037440163
-
Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations
-
Li,W., Ma,B.Y. and Shapiro,B.A. (2003) Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations. Nucleic Acids Res., 31, 629-638.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 629-638
-
-
Li, W.1
Ma, B.Y.2
Shapiro, B.A.3
-
13
-
-
50649115798
-
How RNA unfolds and refolds
-
Li,P.T.X., Vieregg,J. and Tinoco,I. (2008) How RNA unfolds and refolds. Annu. Rev. Biochem., 77, 77-100.
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 77-100
-
-
Li, P.T.X.1
Vieregg, J.2
Tinoco, I.3
-
14
-
-
17844375121
-
Hinge-like motions in RNA kink-turns: the role of the second A-minor motif and nominally unpaired bases
-
Razga,F., Koca,J., Sponer,J. and Leontis,N.B. (2005) Hinge-like motions in RNA kink-turns: the role of the second A-minor motif and nominally unpaired bases. Biophys. J., 88, 3466-3485.
-
(2005)
Biophys. J.
, vol.88
, pp. 3466-3485
-
-
Razga, F.1
Koca, J.2
Sponer, J.3
Leontis, N.B.4
-
15
-
-
70549103338
-
Dependence of A-RNA simulations on the choice of the force field and salt strength
-
Besseova,I., Otyepka,M., Reblova,K. and Sponer,J. (2009) Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys. Chem. Chem. Phys., 11, 10701-10711.
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 10701-10711
-
-
Besseova, I.1
Otyepka, M.2
Reblova, K.3
Sponer, J.4
-
16
-
-
1242347628
-
Theoretical methods for the simulation of nucleic acids
-
Orozco,M., Perez,A., Noy,A. and Luque,F.J. (2003) Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev., 32, 350-364.
-
(2003)
Chem. Soc. Rev.
, vol.32
, pp. 350-364
-
-
Orozco, M.1
Perez, A.2
Noy, A.3
Luque, F.J.4
-
17
-
-
32644451166
-
Molecular dynamics simulations of sarcin-ricin rRNA motif
-
Spackova,N. and Sponer,J. (2006) Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Res., 34, 697-708.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 697-708
-
-
Spackova, N.1
Sponer, J.2
-
18
-
-
33747889715
-
Multiple stages in codon-anticodon recognition: double-trigger mechanisms and geometric constraints
-
Ninio,J. (2006) Multiple stages in codon-anticodon recognition: double-trigger mechanisms and geometric constraints. Biochimie, 88, 963-992.
-
(2006)
Biochimie
, vol.88
, pp. 963-992
-
-
Ninio, J.1
-
19
-
-
4444313551
-
tRNA dynamics on the ribosome during translation
-
Blanchard,S.C., Kim,H.D., Gonzalez,R.L., Puglisi,J.D. and Chu,S. (2004) tRNA dynamics on the ribosome during translation. Proc. Natl Acad. Sci. USA, 101, 12893-12898.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 12893-12898
-
-
Blanchard, S.C.1
Kim, H.D.2
Gonzalez, R.L.3
Puglisi, J.D.4
Chu, S.5
-
20
-
-
33646495214
-
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps
-
Mitra,K. and Frank,J. (2006) Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu. Rev. Biophys. Biomol. Struct., 35, 299-317.
-
(2006)
Annu. Rev. Biophys. Biomol. Struct.
, vol.35
, pp. 299-317
-
-
Mitra, K.1
Frank, J.2
-
21
-
-
33845346092
-
The ribosome and the mechanism of protein synthesis
-
Frank,J. and Spahn,C.M.T. (2006) The ribosome and the mechanism of protein synthesis. Rep. Prog. Phys., 69, 1383-1417.
-
(2006)
Rep. Prog. Phys.
, vol.69
, pp. 1383-1417
-
-
Frank, J.1
Spahn, C.M.T.2
-
22
-
-
4744365694
-
tRNA selection and kinetic proofreading in translation
-
Blanchard,S.C., Gonzalez,R.L., Kim,H.D., Chu,S. and Puglisi,J.D. (2004) tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol., 11, 1008-1014.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 1008-1014
-
-
Blanchard, S.C.1
Gonzalez, R.L.2
Kim, H.D.3
Chu, S.4
Puglisi, J.D.5
-
23
-
-
13744257300
-
Site-specific labeling of the ribosome for single-molecule spectroscopy
-
Dorywalska,M., Blanchard,S.C., Gonzalez,R.L., Kim,H.D., Chu,S. and Puglisi,J.D. (2005) Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res., 33, 182-189.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 182-189
-
-
Dorywalska, M.1
Blanchard, S.C.2
Gonzalez, R.L.3
Kim, H.D.4
Chu, S.5
Puglisi, J.D.6
-
24
-
-
0037029091
-
Ribosome as a molecular machine
-
Spirin,A.S. (2002) Ribosome as a molecular machine. FEBS Lett., 514, 2-10.
-
(2002)
FEBS Lett.
, vol.514
, pp. 2-10
-
-
Spirin, A.S.1
-
25
-
-
33745700326
-
Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme
-
Krasovska,M.V., Sefcikova,J., Reblova,K., Schneider,B., Walter,N.G. and Sponer,J. (2006) Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophys. J., 91, 626-638.
-
(2006)
Biophys. J.
, vol.91
, pp. 626-638
-
-
Krasovska, M.V.1
Sefcikova, J.2
Reblova, K.3
Schneider, B.4
Walter, N.G.5
Sponer, J.6
-
26
-
-
0038539610
-
The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations
-
Auffinger,P., Bielecki,L. and Westhof,E. (2003) The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol., 10, 551-561.
-
(2003)
Chem. Biol.
, vol.10
, pp. 551-561
-
-
Auffinger, P.1
Bielecki, L.2
Westhof, E.3
-
27
-
-
0037764044
-
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E
-
Reblova,K., Spackova,N., Stefl,R., Csaszar,K., Koca,J., Leontis,N.B. and Sponer,J. (2003) Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophys. J., 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
-
28
-
-
33749341539
-
The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50S ribosomal subunits
-
Shankar,N., Kennedy,S.D., Chen,G., Krugh,T.R. and Turner,D.H. (2006) The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50S ribosomal subunits. Biochemistry, 45, 11776-11789.
-
(2006)
Biochemistry
, vol.45
, pp. 11776-11789
-
-
Shankar, N.1
Kennedy, S.D.2
Chen, G.3
Krugh, T.R.4
Turner, D.H.5
-
29
-
-
0037102491
-
The non-Watson-Crick base pairs and their associated isostericity matrices
-
Leontis,N.B., Stombaugh,J. and Westhof,E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., 30, 3497-3531.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3497-3531
-
-
Leontis, N.B.1
Stombaugh, J.2
Westhof, E.3
-
30
-
-
29844448116
-
The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity
-
Brunelle,J.L., Youngman,E.M., Sharma,D. and Green,R. (2006) The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA, 12, 33-39.
-
(2006)
RNA
, vol.12
, pp. 33-39
-
-
Brunelle, J.L.1
Youngman, E.M.2
Sharma, D.3
Green, R.4
-
31
-
-
66149157000
-
Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome
-
Voorhees,R.M., Weixlbaumer,A., Loakes,D., Kelley,A.C. and Ramakrishnan,V. (2009) Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat. Struct. Mol. Biol., 16, 528-533.
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 528-533
-
-
Voorhees, R.M.1
Weixlbaumer, A.2
Loakes, D.3
Kelley, A.C.4
Ramakrishnan, V.5
-
32
-
-
0036214016
-
Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria
-
Hansen,M.A., Kirpekar,F., Ritterbusch,W. and Vester,B. (2002) Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. RNA, 8, 202-213.
-
(2002)
RNA
, vol.8
, pp. 202-213
-
-
Hansen, M.A.1
Kirpekar, F.2
Ritterbusch, W.3
Vester, B.4
-
33
-
-
14844297380
-
U2552 methylation at the ribosomal A-site is a negative modulator of translational accuracy
-
Widerak,M., Kern,R., Malki,A. and Richarme,G. (2005) U2552 methylation at the ribosomal A-site is a negative modulator of translational accuracy. Gene, 347, 109-114.
-
(2005)
Gene
, vol.347
, pp. 109-114
-
-
Widerak, M.1
Kern, R.2
Malki, A.3
Richarme, G.4
-
34
-
-
4444259946
-
Ribosomal RNA kink-turn motif - a flexible molecular hinge
-
Razga,F., Spackova,N., Reblova,K., Koca,J., Leontis,N.B. and Sponer,J. (2004) Ribosomal RNA kink-turn motif - a flexible molecular hinge. J. Biomol. Struct. Dyn., 22, 183-193.
-
(2004)
J. Biomol. Struct. Dyn.
, vol.22
, pp. 183-193
-
-
Razga, F.1
Spackova, N.2
Reblova, K.3
Koca, J.4
Leontis, N.B.5
Sponer, J.6
-
35
-
-
1642458421
-
The kink-turn motif in RNA is dimorphic, and metal ion-dependent
-
Goody,T.A., Melcher,S.E., Norman,D.G. and Lilley,D.M.J. (2004) The kink-turn motif in RNA is dimorphic, and metal ion-dependent. RNA, 10, 254-264.
-
(2004)
RNA
, vol.10
, pp. 254-264
-
-
Goody, T.A.1
Melcher, S.E.2
Norman, D.G.3
Lilley, D.M.J.4
-
36
-
-
0035423087
-
The kink-turn: a new RNA secondary structure motif
-
Klein,D.J., Schmeing,T.M., Moore,P.B. and Steitz,T.A. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J., 20, 4214-4221.
-
(2001)
EMBO J.
, vol.20
, pp. 4214-4221
-
-
Klein, D.J.1
Schmeing, T.M.2
Moore, P.B.3
Steitz, T.A.4
-
37
-
-
0034691576
-
A ratchet-like inter-subunit reorganization of the ribosome during translocation
-
Frank,J. and Agrawal,R.K. (2000) A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature, 406, 318-322.
-
(2000)
Nature
, vol.406
, pp. 318-322
-
-
Frank, J.1
Agrawal, R.K.2
-
38
-
-
34547629747
-
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA
-
Razga,F., Koca,J., Mokdad,A. and Sponer,J. (2007) Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Res., 35, 4007-4017.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 4007-4017
-
-
Razga, F.1
Koca, J.2
Mokdad, A.3
Sponer, J.4
-
39
-
-
34548552815
-
Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine
-
Kouvela,E.C., Gerbanas,G.V., Xaplanteri,M.A., Petropoulos,A.D., Dinos,G.P. and Kalpaxis,D.L. (2007) Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine. Nucleic Acids Res., 35, 5108-5119.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 5108-5119
-
-
Kouvela, E.C.1
Gerbanas, G.V.2
Xaplanteri, M.A.3
Petropoulos, A.D.4
Dinos, G.P.5
Kalpaxis, D.L.6
-
40
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman,D.A., Case,D.A., Caldwell,J.W., Ross,W.S., Cheatham,T.E., Debolt,S., Ferguson,D., Seibel,G. and Kollman,P.A. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun., 91, 1-41.
-
(1995)
Comput. 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.A.9
-
41
-
-
9244260409
-
-
University of California, San Francisco, CA
-
Case,D.A., Darden,T.A., Cheatham,T.E., Simmerling,C.L., Wang,J., Duke,R.E., Luo,R., Merz,K.M., Wang,B., Pearlman,D.A. et al. (2004) Amber 8. University of California, San Francisco, CA.
-
(2004)
Amber 8
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Wang, B.9
Pearlman, D.A.10
-
42
-
-
10844252428
-
-
University of North Carolina, Chapel Hill
-
Duke,R.E. and Pedersen,L.G. (2003) PMEMD 3. University of North Carolina, Chapel Hill.
-
(2003)
PMEMD 3
-
-
Duke, R.E.1
Pedersen, L.G.2
-
43
-
-
33846823909
-
Particle mesh Ewald - an N.LOG(N) method for Ewald sums in large systems
-
Darden,T., York,D. and Pedersen,L. (1993) Particle mesh Ewald - an N.LOG(N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
44
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
-
Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys., 23, 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
45
-
-
0001430231
-
The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition
-
Harvey,S.C., Tan,R.K.Z. and Cheatham,T.E. (1998) The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J. Comput. Chem., 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
-
46
-
-
34247186195
-
-
University of California, San Francisco, CA
-
Case,D.A., Darden,T.A., Cheatham,T.E., Simmerling,C.L., Wang,J., Duke,R.E., Luo,R., Merz,K.M., Pearlman,D.A., Crowley,M. et al. (2006) Amber 9. University of California, San Francisco, CA.
-
(2006)
Amber 9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Pearlman, D.A.9
Crowley, M.10
-
47
-
-
0029878720
-
VMD: visual molecular dynamics
-
Humphrey,W., Dalke,A. and Schulten,K. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 33-38.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
48
-
-
0027441950
-
Essential Dynamics of Proteins
-
Amadei,A., Linssen,A.B.M. and Berendsen,H.J.C. (1993) Essential Dynamics of Proteins. Proteins, 17, 412-425.
-
(1993)
Proteins
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.M.2
Berendsen, H.J.C.3
-
49
-
-
11244269735
-
Interactive essential dynamics
-
Mongan,J. (2004) Interactive essential dynamics. J. Comput. Aided Mol. Des., 18, 433-436.
-
(2004)
J. Comput. Aided Mol. Des.
, vol.18
, pp. 433-436
-
-
Mongan, J.1
-
50
-
-
0345687171
-
A comparative study of motor-protein motions by using a simple elastic-network model
-
Zheng,W.J. and Doniach,S. (2003) A comparative study of motor-protein motions by using a simple elastic-network model. Proc. Natl Acad. Sci. USA, 100, 13253-13258.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 13253-13258
-
-
Zheng, W.J.1
Doniach, S.2
-
51
-
-
3242875210
-
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
-
Suhre,K. and Sanejouand,Y.H. (2004) ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res., 32, W610-W614.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Suhre, K.1
Sanejouand, Y.H.2
-
52
-
-
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., Ferguson,D.M., Spellmeyer,D.C., Fox,T., Caldwell,J.W. and Kollman,P.A. (1995) A Second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 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
Caldwell, J.W.9
Kollman, P.A.10
-
53
-
-
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. and Kollman,P.A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049-1074.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.M.1
Cieplak, P.2
Kollman, P.A.3
-
54
-
-
34250318638
-
Refinenement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
-
Perez,A., Marchan,I., Svozil,D., Sponer,J., Cheatham,T.E., Laughton,C.A. and Orozco,M. (2007) Refinenement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Perez, A.1
Marchan, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
55
-
-
0038475947
-
On the occurrence of the T-loop RNA folding motif in large RNA molecules
-
Krasilnikov,A.S. and Mondragon,A. (2003) On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA, 9, 640-643.
-
(2003)
RNA
, vol.9
, pp. 640-643
-
-
Krasilnikov, A.S.1
Mondragon, A.2
-
56
-
-
0034697987
-
Predicting U-turns in ribosomal RNA with comparative sequence analysis
-
Gutell,R.R., Cannone,J.J., Konings,D. and Gautheret,D. (2000) Predicting U-turns in ribosomal RNA with comparative sequence analysis. J. Mol. Biol., 300, 791-803.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 791-803
-
-
Gutell, R.R.1
Cannone, J.J.2
Konings, D.3
Gautheret, D.4
-
57
-
-
0035942248
-
RNA tertiary interactions in the large ribosomal subunit: the A-minor motif
-
Nissen,P., Ippolito,J.A., Ban,N., Moore,P.B. and Steitz,T.A. (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA, 98, 4899-4903.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 4899-4903
-
-
Nissen, P.1
Ippolito, J.A.2
Ban, N.3
Moore, P.B.4
Steitz, T.A.5
-
58
-
-
33747892834
-
The A-minor motifs in the decoding recognition process
-
Lescoute,A. and Westhof,E. (2006) The A-minor motifs in the decoding recognition process. Biochimie, 88, 993-999.
-
(2006)
Biochimie
, vol.88
, pp. 993-999
-
-
Lescoute, A.1
Westhof, E.2
-
59
-
-
0036314898
-
Sequence and structural conservation in RNA ribose zippers
-
Tamura,M. and Holbrook,S.R. (2002) Sequence and structural conservation in RNA ribose zippers. J. Mol. Biol., 320, 455-474.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 455-474
-
-
Tamura, M.1
Holbrook, S.R.2
-
60
-
-
57549112237
-
Structural dynamics of the ribosome
-
Korostelev,A., Ermolenko,D.N. and Noller,H.F. (2008) Structural dynamics of the ribosome. Curr. Opin. Chem. Biol., 12, 674-683.
-
(2008)
Curr. Opin. Chem. Biol.
, vol.12
, pp. 674-683
-
-
Korostelev, A.1
Ermolenko, D.N.2
Noller, H.F.3
-
61
-
-
33646357500
-
RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics
-
Razga,F., Zacharias,M., Reblova,K., Koca,J. and Sponer,J. (2006) RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. Structure, 14, 825-835.
-
(2006)
Structure
, vol.14
, pp. 825-835
-
-
Razga, F.1
Zacharias, M.2
Reblova, K.3
Koca, J.4
Sponer, J.5
-
62
-
-
27644491082
-
Structures of the bacterial ribosome at 3.5 angstrom resolution
-
Schuwirth,B.S., Borovinskaya,M.A., Hau,C.W., Zhang,W., Vila-Sanjurjo,A., Holton,J.M. and Cate,J.H.D. (2005) Structures of the bacterial ribosome at 3.5 angstrom resolution. Science, 310, 827-834.
-
(2005)
Science
, vol.310
, pp. 827-834
-
-
Schuwirth, B.S.1
Borovinskaya, M.A.2
Hau, C.W.3
Zhang, W.4
Vila-Sanjurjo, A.5
Holton, J.M.6
Cate, J.H.D.7
-
63
-
-
0034578639
-
Comparison of molecular dynamics and harmonic mode calculations on RNA
-
Zacharias,M. (2000) Comparison of molecular dynamics and harmonic mode calculations on RNA. Biopolymers, 54, 547-560.
-
(2000)
Biopolymers
, vol.54
, pp. 547-560
-
-
Zacharias, M.1
-
64
-
-
0036382958
-
Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
-
Tama,F., Wriggers,W. and Brooks,C.L. (2002) Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol., 321, 297-305.
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 297-305
-
-
Tama, F.1
Wriggers, W.2
Brooks, C.L.3
-
65
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
Tama,F., Valle,M., Frank,J. and Brooks,C.L. (2003) Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl Acad. Sci. USA, 100, 9319-9323.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks, C.L.4
-
66
-
-
76649139475
-
Molecular recognition of RNA: challenges for modelling interactions and plasticity
-
Fulle,S. and Gohlke,H. (2010) Molecular recognition of RNA: challenges for modelling interactions and plasticity. J. Mol. Recognit., 23, 220-231.
-
(2010)
J. Mol. Recognit.
, vol.23
, pp. 220-231
-
-
Fulle, S.1
Gohlke, H.2
-
67
-
-
25844441847
-
Comparison of mode analyses at different resolutions applied to nucleic acid systems
-
Van Wynsberghe,A.W. and Cui,Q. (2005) Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys. J., 89, 2939-2949.
-
(2005)
Biophys. J.
, vol.89
, pp. 2939-2949
-
-
Van Wynsberghe, A.W.1
Cui, Q.2
-
68
-
-
0026113980
-
Nonlinear principal component analysis autoassociative neural networks
-
Kramer,M.A. (1991) Nonlinear principal component analysis autoassociative neural networks. AIChE J., 37, 233-243.
-
(1991)
AIChE J.
, vol.37
, pp. 233-243
-
-
Kramer, M.A.1
-
69
-
-
14244271476
-
Molecular dynamics simulation of nucleic acids: successes, limitations, and promise
-
Cheatham,T.E. and Young,M.A. (2000) Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers, 56, 232-256.
-
(2000)
Biopolymers
, vol.56
, pp. 232-256
-
-
Cheatham, T.E.1
Young, M.A.2
-
70
-
-
3042734385
-
Molecular dynamics simulations of guanine quadruplex loops: advances and force field limitations
-
Fadrna,E., Spackova,N., Stefl,R., Koca,J., Cheatham,T.E. and Sponer,J. (2004) Molecular dynamics simulations of guanine quadruplex loops: advances and force field limitations. Biophys. J., 87, 227-242.
-
(2004)
Biophys. J.
, vol.87
, pp. 227-242
-
-
Fadrna, E.1
Spackova, N.2
Stefl, R.3
Koca, J.4
Cheatham, T.E.5
Sponer, J.6
-
71
-
-
0034027592
-
Simulation of the structure and dynamics of nonhelical RNA motifs
-
Zacharias,M. (2000) Simulation of the structure and dynamics of nonhelical RNA motifs. Curr. Opin. Struct. Biol., 10, 311-317.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 311-317
-
-
Zacharias, M.1
-
72
-
-
0034625311
-
Sequence-dependent elastic properties of DNA
-
Lankas,F., Sponer,J., Hobza,P. and Langowski,J. (2000) Sequence-dependent elastic properties of DNA. J. Mol. Biol., 299, 695-709.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 695-709
-
-
Lankas, F.1
Sponer, J.2
Hobza, P.3
Langowski, J.4
-
73
-
-
27644502679
-
Simulating movement of tRNA into the ribosome during decoding
-
Sanbonmatsu,K.Y., Joseph,S. and Tung,C.S. (2005) Simulating movement of tRNA into the ribosome during decoding. Proc. Natl Acad. Sci. USA, 102, 15854-15859.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15854-15859
-
-
Sanbonmatsu, K.Y.1
Joseph, S.2
Tung, C.S.3
-
74
-
-
0038275890
-
Study of the structural dynamics of the E-coli 70S ribosome using real-space refinement
-
Gao,H.X., Sengupta,J., Valle,M., Korostelev,A., Eswar,N., Stagg,S.M., Van Roey,P., Agrawal,R.K., Harvey,S.C., Sali,A. et al. (2003) Study of the structural dynamics of the E-coli 70S ribosome using real-space refinement. Cell, 113, 789-801.
-
(2003)
Cell
, vol.113
, pp. 789-801
-
-
Gao, H.X.1
Sengupta, J.2
Valle, M.3
Korostelev, A.4
Eswar, N.5
Stagg, S.M.6
Van Roey, P.7
Agrawal, R.K.8
Harvey, S.C.9
Sali, A.10
-
75
-
-
24744468042
-
Alteration in location of a conserved GTPase-associated center of the ribosome induced by mutagenesis influences the structure of peptidyltransferase center and activity of elongation factor G
-
Sergiev,P.V., Lesnyak,D.V., Burakovsky,D.E., Kiparisov,S.V., Leonov,A.A., Bogdanov,A.A., Brimacombe,R. and Dontsova,O.A. (2005) Alteration in location of a conserved GTPase-associated center of the ribosome induced by mutagenesis influences the structure of peptidyltransferase center and activity of elongation factor G. J. Biol. Chem., 280, 31882-31889.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 31882-31889
-
-
Sergiev, P.V.1
Lesnyak, D.V.2
Burakovsky, D.E.3
Kiparisov, S.V.4
Leonov, A.A.5
Bogdanov, A.A.6
Brimacombe, R.7
Dontsova, O.A.8
-
76
-
-
33748661254
-
Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities
-
Mokdad,A. and Leontis,N.B. (2006) Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities. Bioinformatics, 22, 2168-2170.
-
(2006)
Bioinformatics
, vol.22
, pp. 2168-2170
-
-
Mokdad, A.1
Leontis, N.B.2
-
77
-
-
41849098954
-
Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes
-
Miyoshi,T. and Uchiumi,T. (2008) Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes. Nucleic Acids Res., 36, 1783-1791.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 1783-1791
-
-
Miyoshi, T.1
Uchiumi, T.2
-
78
-
-
33747881692
-
Alignment/misalignment hypothesis for tRNA selection by the ribosome
-
Sanbonmatsu,K.Y. (2006) Alignment/misalignment hypothesis for tRNA selection by the ribosome. Biochimie, 88, 1075-1089.
-
(2006)
Biochimie
, vol.88
, pp. 1075-1089
-
-
Sanbonmatsu, K.Y.1
-
79
-
-
21244465843
-
Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation
-
Diaconu,M., Kothe,U., Schlunzen,F., Fischer,N., Harms,J.M., Tonevitsky,A.G., Stark,H., Rodnina,M.V. and Wahl,M.C. (2005) Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell, 121, 991-1004.
-
(2005)
Cell
, vol.121
, pp. 991-1004
-
-
Diaconu, M.1
Kothe, U.2
Schlunzen, F.3
Fischer, N.4
Harms, J.M.5
Tonevitsky, A.G.6
Stark, H.7
Rodnina, M.V.8
Wahl, M.C.9
-
80
-
-
70350602056
-
The structure of the ribosome with elongation factor G trapped in the posttranslocational state
-
Gao,Y.G., Selmer,M., Dunham,C.M., Weixlbaumer,A., Kelley,A.C. and Ramakrishnan,V. (2009) The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science, 326, 694-699.
-
(2009)
Science
, vol.326
, pp. 694-699
-
-
Gao, Y.G.1
Selmer, M.2
Dunham, C.M.3
Weixlbaumer, A.4
Kelley, A.C.5
Ramakrishnan, V.6
-
81
-
-
34547111594
-
Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements
-
Kavran,J.M. and Steitz,T.A. (2007) Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. J. Mol. Biol., 371, 1047-1059.
-
(2007)
J. Mol. Biol.
, vol.371
, pp. 1047-1059
-
-
Kavran, J.M.1
Steitz, T.A.2
-
82
-
-
26944498213
-
Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae
-
Kiparisov,S., Petrov,A., Meskauskas,A., Sergiev,P.V., Dontsova,O.A. and Dinman,J.D. (2005) Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae. Mol. Genet. Genomics, 274, 235-247.
-
(2005)
Mol. Genet. Genomics
, vol.274
, pp. 235-247
-
-
Kiparisov, S.1
Petrov, A.2
Meskauskas, A.3
Sergiev, P.V.4
Dontsova, O.A.5
Dinman, J.D.6
-
83
-
-
33845228894
-
An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome
-
Rakauskaite,R. and Dinman,J.D. (2006) An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome. Mol. Cell. Biol., 26, 8992-9002.
-
(2006)
Mol. Cell. Biol.
, vol.26
, pp. 8992-9002
-
-
Rakauskaite, R.1
Dinman, J.D.2
-
84
-
-
25144497020
-
The conserved A-site finger of the 23 S rRNA: just one of the intersubunit bridges or a part of the allosteric communication pathway?
-
Sergiev,P.V., Kiparisov,S.V., Burakovsky,D.E., Lesnyak,D.V., Leonov,A.A., Bogdanov,A.A. and Dontsova,O.A. (2005) The conserved A-site finger of the 23 S rRNA: just one of the intersubunit bridges or a part of the allosteric communication pathway? J. Mol. Biol., 353, 116-123.
-
(2005)
J. Mol. Biol.
, vol.353
, pp. 116-123
-
-
Sergiev, P.V.1
Kiparisov, S.V.2
Burakovsky, D.E.3
Lesnyak, D.V.4
Leonov, A.A.5
Bogdanov, A.A.6
Dontsova, O.A.7
-
85
-
-
33646443228
-
A library of RNA bridges
-
Gao,N. and Frank,J. (2006) A library of RNA bridges. Nat. Chem. Biol., 2, 231-232.
-
(2006)
Nat. Chem. Biol.
, vol.2
, pp. 231-232
-
-
Gao, N.1
Frank, J.2
-
86
-
-
33845958586
-
The a-site finger in 23 S rRNA acts as a functional attenuator for translocation
-
Komoda,T., Sato,N.S., Phelps,S.S., Namba,N., Joseph,S. and Suzuki,T. (2006) The a-site finger in 23 S rRNA acts as a functional attenuator for translocation. J. Biol. Chem., 281, 32303-32309.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 32303-32309
-
-
Komoda, T.1
Sato, N.S.2
Phelps, S.S.3
Namba, N.4
Joseph, S.5
Suzuki, T.6
-
87
-
-
54449100396
-
Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit
-
Piekna-Przybylska,D., Przybylski,P., Baudin-Baillieu,A.S., Rousset,J.P. and Fournier,M.J. (2008) Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit. J. Biol. Chem., 283, 26026-26036.
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 26026-26036
-
-
Piekna-Przybylska, D.1
Przybylski, P.2
Baudin-Baillieu, A.S.3
Rousset, J.P.4
Fournier, M.J.5
-
88
-
-
54049116765
-
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome
-
Agirrezabala,X., Lei,J.L., Brunelle,J.L., Ortiz-Meoz,R.F., Green,R. and Frank,J. (2008) Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol. Cell, 32, 190-197.
-
(2008)
Mol. Cell
, vol.32
, pp. 190-197
-
-
Agirrezabala, X.1
Lei, J.L.2
Brunelle, J.L.3
Ortiz-Meoz, R.F.4
Green, R.5
Frank, J.6
-
89
-
-
0035805213
-
Crystal structure of the ribosome at 5.5 angstrom resolution
-
Yusupov,M.M., Yusupova,G.Z., Baucom,A., Lieberman,K., Earnest,T.N., Cate,J.H.D. and Noller,H.F. (2001) Crystal structure of the ribosome at 5.5 angstrom resolution. Science, 292, 883-896.
-
(2001)
Science
, vol.292
, pp. 883-896
-
-
Yusupov, M.M.1
Yusupova, G.Z.2
Baucom, A.3
Lieberman, K.4
Earnest, T.N.5
Cate, J.H.D.6
Noller, H.F.7
-
90
-
-
77950366458
-
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and cryo-EM
-
Reblova,K., Razga,F., Li,W., Gao,H., Frank,J. and Sponer,J. (2009) Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and cryo-EM. Nucleic Acids Res., 38, 1325-1340.
-
(2009)
Nucleic Acids Res.
, vol.38
, pp. 1325-1340
-
-
Reblova, K.1
Razga, F.2
Li, W.3
Gao, H.4
Frank, J.5
Sponer, J.6
-
91
-
-
2942615089
-
The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit
-
Klein,D.J., Moore,P.B. and Steitz,T.A. (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol., 340, 141-177.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 141-177
-
-
Klein, D.J.1
Moore, P.B.2
Steitz, T.A.3
-
92
-
-
69849114530
-
Classification and energetics of the base-phosphate interactions in RNA
-
Zirbel,C.L., Sponer,J.E., Sponer,J., Stombaugh,J. and Leontis,N.B. (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4898-4918
-
-
Zirbel, C.L.1
Sponer, J.E.2
Sponer, J.3
Stombaugh, J.4
Leontis, N.B.5
-
93
-
-
0035977093
-
High resolution structure of the large ribosomal subunit from a mesophilic eubacterium
-
Harms,J., Schluenzen,F., Zarivach,R., Bashan,A., Gat,S., Agmon,I., Bartels,H., Franceschi,F. and Yonath,A. (2001) High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell, 107, 679-688.
-
(2001)
Cell
, vol.107
, pp. 679-688
-
-
Harms, J.1
Schluenzen, F.2
Zarivach, R.3
Bashan, A.4
Gat, S.5
Agmon, I.6
Bartels, H.7
Franceschi, F.8
Yonath, A.9
-
94
-
-
49649099901
-
Structural basis for translation termination on the 70S ribosome
-
Laurberg,M., Asahara,H., Korostelev,A., Zhu,J.Y., Trakhanov,S. and Noller,H.F. (2008) Structural basis for translation termination on the 70S ribosome. Nature, 454, 852-857.
-
(2008)
Nature
, vol.454
, pp. 852-857
-
-
Laurberg, M.1
Asahara, H.2
Korostelev, A.3
Zhu, J.Y.4
Trakhanov, S.5
Noller, H.F.6
|