-
1
-
-
84865084480
-
Molecular Dynamics Simulations of G-DNA and Perspectives on the Simulation of Nucleic Acid Structures
-
Sponer, J.; Cang, X. H.; Cheatham, T. E. Molecular Dynamics Simulations of G-DNA and Perspectives on the Simulation of Nucleic Acid Structures Methods 2012, 57, 25-39
-
(2012)
Methods
, vol.57
, pp. 25-39
-
-
Sponer, J.1
Cang, X.H.2
Cheatham, T.E.3
-
2
-
-
84860477162
-
Frontiers in Molecular Dynamics Simulations of DNA
-
Perez, A.; Luque, F. J.; Orozco, M. Frontiers in Molecular Dynamics Simulations of DNA Acc. Chem. Res. 2011, 45, 196-205
-
(2011)
Acc. Chem. Res.
, vol.45
, pp. 196-205
-
-
Perez, A.1
Luque, F.J.2
Orozco, M.3
-
3
-
-
84861765128
-
Computational Studies of Molecular Machines: The Ribosome
-
Sanbonmatsu, K. Y. Computational Studies of Molecular Machines: The Ribosome Curr. Opin. Struct. Biol. 2012, 22, 168-174
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 168-174
-
-
Sanbonmatsu, K.Y.1
-
4
-
-
75449112058
-
Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe in
-
Ditzler, M. A.; Otyepka, M.; Sponer, J.; Walter, N. G. Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In Acc. Chem. Res. 2009, 43, 40-47
-
(2009)
Acc. Chem. Res.
, vol.43
, pp. 40-47
-
-
Ditzler, M.A.1
Otyepka, M.2
Sponer, J.3
Walter, N.G.4
-
5
-
-
33847318371
-
Molecular Dynamics Simulations of RNA: An in Silico Single Molecule Approach
-
McDowell, S. E.; Spackova, N.; Sponer, J.; Walter, N. G. Molecular Dynamics Simulations of RNA: An In Silico Single Molecule Approach Biopolymers 2007, 85, 169-184
-
(2007)
Biopolymers
, vol.85
, pp. 169-184
-
-
McDowell, S.E.1
Spackova, N.2
Sponer, J.3
Walter, N.G.4
-
6
-
-
34347404466
-
Nucleic Acid Solvation: From Outside to Insight
-
Auffinger, P.; Hashem, Y. Nucleic Acid Solvation: From Outside to Insight Curr. Opin. Struct. Biol. 2007, 17, 325-333
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 325-333
-
-
Auffinger, P.1
Hashem, Y.2
-
8
-
-
84861367246
-
Biomolecular Simulation: A Computational Microscope for Molecular Biology
-
Dror, R. O.; Dirks, R. M.; Grossman, J. P.; Xu, H.; Shaw, D. E. Biomolecular Simulation: A Computational Microscope for Molecular Biology Annu. Rev. Biophys. 2012, 41, 429-452
-
(2012)
Annu. Rev. Biophys.
, vol.41
, pp. 429-452
-
-
Dror, R.O.1
Dirks, R.M.2
Grossman, J.P.3
Xu, H.4
Shaw, D.E.5
-
9
-
-
84884192184
-
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
-
Salomon-Ferrer, R.; Goetz, A. W.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald J. Chem. Theory Comput. 2013, 9, 3878-3888
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3878-3888
-
-
Salomon-Ferrer, R.1
Goetz, A.W.2
Poole, D.3
Le Grand, S.4
Walker, R.C.5
-
10
-
-
70450248170
-
A Systematic Molecular Dynamics Study of Nearest-Neighbor Effects on Base Pair and Base Pair Step Conformations and Fluctuations in B-DNA
-
Lavery, R.; Zakrzewska, K.; Beveridge, D.; Bishop, T. C.; Case, D. A.; Cheatham, T.; Dixit, S.; Jayaram, B.; Lankas, F.; Laughton, C. A Systematic Molecular Dynamics Study of Nearest-Neighbor Effects on Base Pair and Base Pair Step Conformations and Fluctuations in B-DNA Nucleic Acids Res. 2010, 38, 299-313
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 299-313
-
-
Lavery, R.1
Zakrzewska, K.2
Beveridge, D.3
Bishop, T.C.4
Case, D.A.5
Cheatham, T.6
Dixit, S.7
Jayaram, B.8
Lankas, F.9
Laughton, C.10
-
11
-
-
84867761593
-
Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration
-
Besseova, I.; Banas, P.; Kuehrova, P.; Kosinova, P.; Otyepka, M.; Sponer, J. Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration J. Phys. Chem. B 2012, 116, 9899-9916
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 9899-9916
-
-
Besseova, I.1
Banas, P.2
Kuehrova, P.3
Kosinova, P.4
Otyepka, M.5
Sponer, J.6
-
12
-
-
79960650298
-
Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised π Torsions
-
Yildirim, I.; Stern, H. A.; Tubbs, J. D.; Kennedy, S. D.; Turner, D. H. Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised π Torsions J. Phys. Chem. B 2011, 115, 9261-9270
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 9261-9270
-
-
Yildirim, I.1
Stern, H.A.2
Tubbs, J.D.3
Kennedy, S.D.4
Turner, D.H.5
-
13
-
-
84873670994
-
The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics
-
Tubbs, J. D.; Condon, D. E.; Kennedy, S. D.; Hauser, M.; Bevilacqua, P. C.; Turner, D. H. The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics Biochemistry 2013, 52, 996-1010
-
(2013)
Biochemistry
, vol.52
, pp. 996-1010
-
-
Tubbs, J.D.1
Condon, D.E.2
Kennedy, S.D.3
Hauser, M.4
Bevilacqua, P.C.5
Turner, D.H.6
-
14
-
-
84876471104
-
Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations
-
Henriksen, N. M.; Roe, D. R.; Cheatham, T. E. Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations J. Phys. Chem. B 2013, 117, 4014-4027
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 4014-4027
-
-
Henriksen, N.M.1
Roe, D.R.2
Cheatham, T.E.3
-
15
-
-
84892604842
-
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide
-
Bergonzo, C.; Henriksen, N. M.; Roe, D. R.; Swails, J. M.; Roitberg, A. E.; Cheatham, T. E. Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide J. Chem. Theory Comput. 2013, 10, 492-499
-
(2013)
J. Chem. Theory Comput.
, vol.10
, pp. 492-499
-
-
Bergonzo, C.1
Henriksen, N.M.2
Roe, D.R.3
Swails, J.M.4
Roitberg, A.E.5
Cheatham, T.E.6
-
16
-
-
78249249624
-
Multiple Routes to Characterize the Folding of a Small DNA Hairpin
-
Portella, G.; Orozco, M. Multiple Routes to Characterize the Folding of a Small DNA Hairpin Angew. Chem., Int. Ed. 2010, 49, 7673-7676
-
(2010)
Angew. Chem., Int. Ed.
, vol.49
, pp. 7673-7676
-
-
Portella, G.1
Orozco, M.2
-
17
-
-
78651294111
-
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
-
Banas, P.; Hollas, D.; Zgarbova, M.; Jurecka, P.; Orozco, M.; Cheatham, T. E.; Sponer, J.; Otyepka, M. Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins J. Chem. Theory Comput. 2010, 6, 3836-3849
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3836-3849
-
-
Banas, P.1
Hollas, D.2
Zgarbova, M.3
Jurecka, P.4
Orozco, M.5
Cheatham, T.E.6
Sponer, J.7
Otyepka, M.8
-
18
-
-
84875989318
-
Computer Folding of RNA Tetraloops? Are We There Yet?
-
Kuehrova, P.; Banas, P.; Best, R. B.; Sponer, J.; Otyepka, M. Computer Folding of RNA Tetraloops? Are We There Yet? J. Chem. Theory Comput. 2013, 9, 2115-2125
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2115-2125
-
-
Kuehrova, P.1
Banas, P.2
Best, R.B.3
Sponer, J.4
Otyepka, M.5
-
19
-
-
84885818229
-
High-Resolution Reversible Folding of Hyperstable RNA Tetraloops Using Molecular Dynamics Simulations
-
Chen, A. A.; Garcia, A. E. High-Resolution Reversible Folding of Hyperstable RNA Tetraloops Using Molecular Dynamics Simulations Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 16820-16825
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 16820-16825
-
-
Chen, A.A.1
Garcia, A.E.2
-
20
-
-
73349099062
-
Single Stranded Loops of Quadruplex DNA as Key Benchmark for Testing Nucleic Acids Force Fields
-
Fadrna, E.; Spackova, N.; Sarzynska, J.; Koca, J.; Orozco, M.; Cheatham, T. E.; Kulinski, T.; Sponer, J. Single Stranded Loops of Quadruplex DNA as Key Benchmark for Testing Nucleic Acids Force Fields J. Chem. Theory Comput. 2009, 5, 2514-2530
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2514-2530
-
-
Fadrna, E.1
Spackova, N.2
Sarzynska, J.3
Koca, J.4
Orozco, M.5
Cheatham, T.E.6
Kulinski, T.7
Sponer, J.8
-
21
-
-
84863658763
-
Reference Simulations of Noncanonical Nucleic Acids with Different Chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA
-
Krepl, M.; Zgarbova, M.; Stadlbauer, P.; Otyepka, M.; Banas, P.; Koca, J.; Cheatham, T. E.; Jurecka, P.; Sponer, J. Reference Simulations of Noncanonical Nucleic Acids with Different Chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA J. Chem. Theory Comput. 2012, 8, 2506-2520
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2506-2520
-
-
Krepl, M.1
Zgarbova, M.2
Stadlbauer, P.3
Otyepka, M.4
Banas, P.5
Koca, J.6
Cheatham, T.E.7
Jurecka, P.8
Sponer, J.9
-
22
-
-
17944388579
-
Molecular Dynamics Simulations of RNA Kissing-Loop Motifs Reveal Structural Dynamics and Formation of Cation-Binding Pockets
-
Reblova, K.; Spackova, N.; Sponer, J. E.; Koca, J.; Sponer, J. Molecular Dynamics Simulations of RNA Kissing-Loop Motifs Reveal Structural Dynamics and Formation of Cation-Binding Pockets Nucleic Acids Res. 2003, 31, 6942-6952
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6942-6952
-
-
Reblova, K.1
Spackova, N.2
Sponer, J.E.3
Koca, J.4
Sponer, J.5
-
23
-
-
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.; Sponer, J. Non-Watson-Crick Basepairing and Hydration in RNA Motifs: Molecular Dynamics of 5S rRNA Loop E Biophys. J. 2003, 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
-
24
-
-
0346366808
-
2+ Ion-Binding Sites in the 5S rRNA Loop e Inferred from Molecular Dynamics Simulations
-
2+ Ion-Binding Sites in the 5S rRNA Loop E Inferred from Molecular Dynamics Simulations J. Mol. Biol. 2004, 335, 555-571
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 555-571
-
-
Auffinger, P.1
Bielecki, L.2
Westhof, E.3
-
25
-
-
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.; Leontis, N. B. Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-Minor Motif and Nominally Unpaired Bases Biophys. J. 2005, 88, 3466-3485
-
(2005)
Biophys. J.
, vol.88
, pp. 3466-3485
-
-
Razga, F.1
Koca, J.2
Sponer, J.3
Leontis, N.B.4
-
26
-
-
80052480507
-
Interactions of Cations with RNA Loop-Loop Complexes
-
Singh, A.; Sethaphong, L.; Yingling, Y. G. Interactions of Cations with RNA Loop-Loop Complexes Biophys. J. 2011, 101, 727-735
-
(2011)
Biophys. J.
, vol.101
, pp. 727-735
-
-
Singh, A.1
Sethaphong, L.2
Yingling, Y.G.3
-
27
-
-
84871062858
-
Comparing Aminoglycoside Binding Sites in Bacterial Ribosomal RNA and Aminoglycoside Modifying Enzymes
-
Romanowska, J.; Reuter, N.; Trylska, J. Comparing Aminoglycoside Binding Sites in Bacterial Ribosomal RNA and Aminoglycoside Modifying Enzymes Proteins: Struct., Funct., Bioinf. 2013, 81, 63-80
-
(2013)
Proteins: Struct., Funct., Bioinf.
, vol.81
, pp. 63-80
-
-
Romanowska, J.1
Reuter, N.2
Trylska, J.3
-
28
-
-
84888604588
-
Isosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin-Ricin Internal Loop
-
Havrila, M.; Reblova, K.; Zirbel, C. L.; Leontis, N. B.; Sponer, J. Isosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin-Ricin Internal Loop J. Phys. Chem. B 2013, 117, 14302-14319
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 14302-14319
-
-
Havrila, M.1
Reblova, K.2
Zirbel, C.L.3
Leontis, N.B.4
Sponer, J.5
-
29
-
-
84896292945
-
A Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA Pairs in RNA
-
Aytenfisu, A. H.; Spasic, A.; Seetin, M. G.; Serafini, J.; Mathews, D. H. A Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA Pairs in RNA J. Chem. Theory Comput. 2014, 10, 1292-1301
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1292-1301
-
-
Aytenfisu, A.H.1
Spasic, A.2
Seetin, M.G.3
Serafini, J.4
Mathews, D.H.5
-
30
-
-
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.; Sponer, J. Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme Biophys. J. 2006, 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
-
31
-
-
33748628543
-
Trapped Water Molecules Are Essential to Structural Dynamics and Function of a Ribozyme
-
Rhodes, M. M.; Reblova, K.; Sponer, J.; Walter, N. G. Trapped Water Molecules Are Essential to Structural Dynamics and Function of a Ribozyme Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 13380-13385
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 13380-13385
-
-
Rhodes, M.M.1
Reblova, K.2
Sponer, J.3
Walter, N.G.4
-
32
-
-
41449099097
-
2+ in Hammerhead Ribozyme Catalysis from Molecular Simulation
-
2+ in Hammerhead Ribozyme Catalysis from Molecular Simulation J. Am. Chem. Soc. 2008, 130, 3053-3064
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 3053-3064
-
-
Lee, T.-S.1
Lopez, C.S.2
Giambasu, G.M.3
Martick, M.4
Scott, W.G.5
York, D.M.6
-
33
-
-
77954332068
-
Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics
-
Banas, P.; Walter, N. G.; Sponer, J.; Otyepka, M. Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics J. Phys. Chem. B 2010, 114, 8701-8712
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 8701-8712
-
-
Banas, P.1
Walter, N.G.2
Sponer, J.3
Otyepka, M.4
-
34
-
-
78649640602
-
Deciphering the Role of Glucosamine-6-Phosphate in the Riboswitch Action of glmS Ribozyme
-
Xin, Y.; Hamelberg, D. Deciphering the Role of Glucosamine-6-Phosphate in the Riboswitch Action of glmS Ribozyme RNA 2010, 16, 2455-2463
-
(2010)
RNA
, vol.16
, pp. 2455-2463
-
-
Xin, Y.1
Hamelberg, D.2
-
35
-
-
80054929125
-
Characterization of the Structure and Dynamics of the HDV Ribozyme in Different Stages Along the Reaction Path
-
Lee, T.-S.; Giambasu, G. M.; Harris, M. E.; York, D. M. Characterization of the Structure and Dynamics of the HDV Ribozyme in Different Stages Along the Reaction Path J. Phys. Chem. Lett. 2011, 2, 2538-2543
-
(2011)
J. Phys. Chem. Lett.
, vol.2
, pp. 2538-2543
-
-
Lee, T.-S.1
Giambasu, G.M.2
Harris, M.E.3
York, D.M.4
-
36
-
-
79953205188
-
Metal Binding Motif in the Active Site of the HDV Ribozyme Binds Divalent and Monovalent Ions
-
Veeraraghavan, N.; Ganguly, A.; Chen, J.-H.; Bevilacqua, P. C.; Hammes-Schiffer, S.; Golden, B. L. Metal Binding Motif in the Active Site of the HDV Ribozyme Binds Divalent and Monovalent Ions Biochemistry 2011, 50, 2672-2682
-
(2011)
Biochemistry
, vol.50
, pp. 2672-2682
-
-
Veeraraghavan, N.1
Ganguly, A.2
Chen, J.-H.3
Bevilacqua, P.C.4
Hammes-Schiffer, S.5
Golden, B.L.6
-
37
-
-
69049108817
-
Molecular Dynamics Simulation Study of the Binding of Purine Bases to the Aptamer Domain of the Guanine Sensing Riboswitch
-
Villa, A.; Woehnert, J.; Stock, G. Molecular Dynamics Simulation Study of the Binding of Purine Bases to the Aptamer Domain of the Guanine Sensing Riboswitch Nucleic Acids Res. 2009, 37, 4774-4786
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4774-4786
-
-
Villa, A.1
Woehnert, J.2
Stock, G.3
-
38
-
-
84867801144
-
Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study
-
Banas, P.; Sklenovsky, P.; Wedekind, J. E.; Sponer, J.; Otyepka, M. Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study J. Phys. Chem. B 2012, 116, 12721-12734
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 12721-12734
-
-
Banas, P.1
Sklenovsky, P.2
Wedekind, J.E.3
Sponer, J.4
Otyepka, M.5
-
39
-
-
77950350987
-
Atomistic Basis for the On-Off Signaling Mechanism in SAM-II Riboswitch
-
Kelley, J. M.; Hamelberg, D. Atomistic Basis for the On-Off Signaling Mechanism in SAM-II Riboswitch Nucleic Acids Res. 2010, 38, 1392-1400
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 1392-1400
-
-
Kelley, J.M.1
Hamelberg, D.2
-
40
-
-
84855984817
-
Atomic-Level Insights into Metabolite Recognition and Specificity of the SAM-II Riboswitch
-
Doshi, U.; Kelley, J. M.; Hamelberg, D. Atomic-Level Insights into Metabolite Recognition and Specificity of the SAM-II Riboswitch RNA 2012, 18, 300-307
-
(2012)
RNA
, vol.18
, pp. 300-307
-
-
Doshi, U.1
Kelley, J.M.2
Hamelberg, D.3
-
41
-
-
84885985615
-
Ligand-Induced Stabilization of the Aptamer Terminal Helix in the add Adenine Riboswitch
-
Di Palma, F.; Colizzi, F.; Bussi, G. Ligand-Induced Stabilization of the Aptamer Terminal Helix in the add Adenine Riboswitch RNA 2013, 19, 1517-1524
-
(2013)
RNA
, vol.19
, pp. 1517-1524
-
-
Di Palma, F.1
Colizzi, F.2
Bussi, G.3
-
42
-
-
84892774485
-
Interconversion between Parallel and Antiparallel Conformations of a 4H RNA junction in Domain 3 of Foot-and-Mouth Disease Virus IRES Captured by Dynamics Simulations
-
Jung, S.; Schlick, T. Interconversion between Parallel and Antiparallel Conformations of a 4H RNA junction in Domain 3 of Foot-and-Mouth Disease Virus IRES Captured by Dynamics Simulations Biophys. J. 2014, 106, 447-458
-
(2014)
Biophys. J.
, vol.106
, pp. 447-458
-
-
Jung, S.1
Schlick, T.2
-
43
-
-
84864479919
-
Structure and Mechanical Properties of the Ribosomal L1 Stalk Three-Way Junction
-
Reblova, K.; Sponer, J.; Lankas, F. Structure and Mechanical Properties of the Ribosomal L1 Stalk Three-Way Junction Nucleic Acids Res. 2012, 40, 6290-6303
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 6290-6303
-
-
Reblova, K.1
Sponer, J.2
Lankas, F.3
-
44
-
-
27644502679
-
Simulating Movement of tRNA into the Ribosome during Decoding
-
Sanbonmatsu, K. Y.; Joseph, S.; Tung, C.-S. Simulating Movement of tRNA into the Ribosome During Decoding Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 15854-15859
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 15854-15859
-
-
Sanbonmatsu, K.Y.1
Joseph, S.2
Tung, C.-S.3
-
45
-
-
42949089487
-
Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
-
Trabuco, L. G.; Villa, E.; Mitra, K.; Frank, J.; Schulten, K. Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics Structure 2008, 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
-
46
-
-
77956935085
-
The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle
-
Trabuco, L. G.; Schreiner, E.; Eargle, J.; Cornish, P.; Ha, T.; Luthey-Schulten, Z.; Schulten, K. The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle J. Mol. Biol. 2010, 402, 741-760
-
(2010)
J. Mol. Biol.
, vol.402
, pp. 741-760
-
-
Trabuco, L.G.1
Schreiner, E.2
Eargle, J.3
Cornish, P.4
Ha, T.5
Luthey-Schulten, Z.6
Schulten, K.7
-
47
-
-
34247520870
-
Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution Studied by Molecular Dynamics Simulation
-
Roccatano, D.; Barthel, A.; Zacharias, M. Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution Studied by Molecular Dynamics Simulation Biopolymers 2007, 85, 407-421
-
(2007)
Biopolymers
, vol.85
, pp. 407-421
-
-
Roccatano, D.1
Barthel, A.2
Zacharias, M.3
-
48
-
-
84888223867
-
Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations
-
Portella, G.; Battistini, F.; Orozco, M. Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations PLoS Comput. Biol. 2013, 9, e1003354
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. 1003354
-
-
Portella, G.1
Battistini, F.2
Orozco, M.3
-
49
-
-
84855661433
-
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
-
Hart, K.; Foloppe, N.; Baker, C. M.; Denning, E. J.; Nilsson, L.; MacKerell, A. D. Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium J. Chem. Theory Comput. 2011, 8, 348-362
-
(2011)
J. Chem. Theory Comput.
, vol.8
, pp. 348-362
-
-
Hart, K.1
Foloppe, N.2
Baker, C.M.3
Denning, E.J.4
Nilsson, L.5
MacKerell, A.D.6
-
50
-
-
84877729731
-
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
-
Zgarbova, M.; Luque, F. J.; Sponer, J.; Cheatham, T. E.; Otyepka, M.; Jurecka, P. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters J. Chem. Theory Comput. 2013, 9, 2339-2354
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2339-2354
-
-
Zgarbova, M.1
Luque, F.J.2
Sponer, J.3
Cheatham, T.E.4
Otyepka, M.5
Jurecka, P.6
-
51
-
-
79955484353
-
Impact of 2′-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-Atom Additive Force Field for RNA
-
Denning, E. J.; Priyakumar, U. D.; Nilsson, L.; Mackerell, A. D. Impact of 2′-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-Atom Additive Force Field for RNA J. Comput. Chem. 2011, 32, 1929-1943
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 1929-1943
-
-
Denning, E.J.1
Priyakumar, U.D.2
Nilsson, L.3
MacKerell, A.D.4
-
52
-
-
80052820313
-
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
-
Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T. E.; Jurecka, P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles J. Chem. Theory Comput. 2011, 7, 2886-2902
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2886-2902
-
-
Zgarbova, M.1
Otyepka, M.2
Sponer, J.3
Mladek, A.4
Banas, P.5
Cheatham, T.E.6
Jurecka, P.7
-
53
-
-
84867973569
-
The DNA and RNA Sugar-Phosphate Backbone Emerges as the Key Player. An Overview of Quantum-Chemical, Structural Biology and Simulation Studies
-
Sponer, J.; Mladek, A.; Sponer, J. E.; Svozil, D.; Zgarbova, M.; Banas, P.; Jurecka, P.; Otyepka, M. The DNA and RNA Sugar-Phosphate Backbone Emerges as the Key Player. An Overview of Quantum-Chemical, Structural Biology and Simulation Studies Phys. Chem. Chem. Phys. 2012, 14, 15257-15277
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 15257-15277
-
-
Sponer, J.1
Mladek, A.2
Sponer, J.E.3
Svozil, D.4
Zgarbova, M.5
Banas, P.6
Jurecka, P.7
Otyepka, M.8
-
54
-
-
84892616086
-
Energies and 2′-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations
-
Mladek, A.; Banas, P.; Jurecka, P.; Otyepka, M.; Zgarbova, M.; Sponer, J. Energies and 2′-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations J. Chem. Theory Comput. 2014, 10, 463-480
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 463-480
-
-
Mladek, A.1
Banas, P.2
Jurecka, P.3
Otyepka, M.4
Zgarbova, M.5
Sponer, J.6
-
55
-
-
84879754496
-
Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations
-
Sponer, J.; Mladek, A.; Spackova, N.; Cang, X. H.; Cheatham, T. E.; Grimme, S. Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations J. Am. Chem. Soc. 2013, 135, 9785-9796
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 9785-9796
-
-
Sponer, J.1
Mladek, A.2
Spackova, N.3
Cang, X.H.4
Cheatham, T.E.5
Grimme, S.6
-
56
-
-
84877712594
-
Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops
-
Krepl, M.; Reblova, K.; Koca, J.; Sponer, J. Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops J. Phys. Chem. B 2013, 117, 5540-5555
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 5540-5555
-
-
Krepl, M.1
Reblova, K.2
Koca, J.3
Sponer, J.4
-
57
-
-
84896304097
-
Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations
-
Gkionis, K.; Kruse, H.; Platts, J. A.; Mladek, A.; Koca, J.; Sponer, J. Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations J. Chem. Theory Comput. 2014, 10, 1326-1340
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1326-1340
-
-
Gkionis, K.1
Kruse, H.2
Platts, J.A.3
Mladek, A.4
Koca, J.5
Sponer, J.6
-
58
-
-
79961199372
-
Explaining the Varied Glycosidic Conformational, G-Tract Length and Sequence Preferences for Anti-Parallel G-Quadruplexes
-
Cang, X. H.; Sponer, J.; Cheatham, T. E. Explaining the Varied Glycosidic Conformational, G-Tract Length and Sequence Preferences for Anti-Parallel G-Quadruplexes Nucleic Acids Res. 2011, 39, 4499-4512
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 4499-4512
-
-
Cang, X.H.1
Sponer, J.2
Cheatham, T.E.3
-
59
-
-
77952472539
-
+ Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme
-
+ Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme J. Phys. Chem. B 2010, 114, 6642-6652
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 6642-6652
-
-
Mlynsky, V.1
Banas, P.2
Hollas, D.3
Reblova, K.4
Walter, N.G.5
Sponer, J.6
Otyepka, M.7
-
60
-
-
78149461723
-
Coarse-Grained Models to Study Dynamics of Nanoscale Biomolecules and Their Applications to the Ribosome
-
Trylska, J. Coarse-Grained Models to Study Dynamics of Nanoscale Biomolecules and Their Applications to the Ribosome J. Phys.: Condens. Matter 2010, 22, 453101
-
(2010)
J. Phys.: Condens. Matter
, vol.22
, pp. 453101
-
-
Trylska, J.1
-
61
-
-
77957159348
-
Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome
-
Whitford, P. C.; Onuchic, J. N.; Sanbonmatsu, K. Y. Connecting Energy Landscapes with Experimental Rates for Aminoacyl-tRNA Accommodation in the Ribosome J. Am. Chem. Soc. 2010, 132, 13170-13171
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 13170-13171
-
-
Whitford, P.C.1
Onuchic, J.N.2
Sanbonmatsu, K.Y.3
-
62
-
-
59649095963
-
A Short Guide for Molecular Dynamics Simulations of RNA Systems
-
Hashem, Y.; Auffinger, P. A Short Guide for Molecular Dynamics Simulations of RNA Systems Methods 2009, 47, 187-197
-
(2009)
Methods
, vol.47
, pp. 187-197
-
-
Hashem, Y.1
Auffinger, P.2
-
63
-
-
0031535392
-
Water Exchange on Magnesium(II) in Aqueous Solution: A Variable Temperature and Pressure O-17 NMR Study
-
Bleuzen, A.; Pittet, P. A.; Helm, L.; Merbach, A. E. Water Exchange on Magnesium(II) in Aqueous Solution: A Variable Temperature and Pressure O-17 NMR Study Magn. Reson. Chem. 1997, 35, 765-773
-
(1997)
Magn. Reson. Chem.
, vol.35
, pp. 765-773
-
-
Bleuzen, A.1
Pittet, P.A.2
Helm, L.3
Merbach, A.E.4
-
64
-
-
2442641641
-
A Conformational Switch Controls Hepatitis Delta Virus Ribozyme Catalysis
-
Ke, A.; Zhou, K.; Ding, F.; Cate, J. H. D.; 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.D.4
Doudna, J.A.5
-
65
-
-
52349114415
-
General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility
-
Banas, P.; Rulisek, L.; Hanosova, V.; Svozil, D.; Walter, N. G.; Sponer, J.; Otyepka, M. General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility J. Phys. Chem. B 2008, 112, 11177-11187
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 11177-11187
-
-
Banas, P.1
Rulisek, L.2
Hanosova, V.3
Svozil, D.4
Walter, N.G.5
Sponer, J.6
Otyepka, M.7
-
66
-
-
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
-
67
-
-
77955258795
-
A 1.9 Angstrom Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage
-
Chen, J.-H.; Yajima, R.; Chadalavada, D. M.; Chase, E.; Bevilacqua, P. C.; Golden, B. L. A 1.9 Angstrom Crystal Structure of the HDV Ribozyme Precleavage Suggests both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage Biochemistry 2010, 49, 6508-6518
-
(2010)
Biochemistry
, vol.49
, pp. 6508-6518
-
-
Chen, J.-H.1
Yajima, R.2
Chadalavada, D.M.3
Chase, E.4
Bevilacqua, P.C.5
Golden, B.L.6
-
68
-
-
0028864424
-
Studies of Base Pair Kinetics by NMR Measurement of Proton Exchange
-
In; Thomas, L. J. Academic Press: San Diego, CA, Vol. - 413
-
Gueron, M.; Leroy, J.-L. Studies of Base Pair Kinetics by NMR Measurement of Proton Exchange. In Methods of Enzymology; Thomas, L. J., Ed.; Academic Press: San Diego, CA, 1995; Vol. 261; pp 383-413.
-
(1995)
Methods of Enzymology
, vol.261
, pp. 383
-
-
Gueron, M.1
Leroy, J.-L.2
-
69
-
-
77950141432
-
An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 ′-UAA/5 ′-GAN Internal Loops Studied by Molecular Dynamics Methods
-
Reblova, K.; Strelcova, Z.; Kulhanek, P.; Besseova, I.; Mathews, D. H.; Van Nostrand, K.; Yildirim, I.; Turner, D. H.; Sponer, J. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 ′-UAA/5 ′-GAN Internal Loops Studied by Molecular Dynamics Methods J. Chem. Theory Comput. 2010, 6, 910-929
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 910-929
-
-
Reblova, K.1
Strelcova, Z.2
Kulhanek, P.3
Besseova, I.4
Mathews, D.H.5
Van Nostrand, K.6
Yildirim, I.7
Turner, D.H.8
Sponer, J.9
-
70
-
-
80052800450
-
Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group i Intron Reverse Kink-Turn Motifs
-
Sklenovsky, P.; Florova, P.; Banas, P.; Reblova, K.; Lankas, F.; Otyepka, M.; Sponer, J. Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs J. Chem. Theory Comput. 2011, 7, 2963-2980
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2963-2980
-
-
Sklenovsky, P.1
Florova, P.2
Banas, P.3
Reblova, K.4
Lankas, F.5
Otyepka, M.6
Sponer, J.7
-
71
-
-
67649363284
-
Molecular Simulation Studies of Monovalent Counterion-Mediated Interactions in a Model RNA Kissing Loop
-
Chen, A. A.; Draper, D. E.; Pappu, R. V. Molecular Simulation Studies of Monovalent Counterion-Mediated Interactions in a Model RNA Kissing Loop J. Mol. Biol. 2009, 390, 805-819
-
(2009)
J. Mol. Biol.
, vol.390
, pp. 805-819
-
-
Chen, A.A.1
Draper, D.E.2
Pappu, R.V.3
-
72
-
-
0001616080
-
Replica-Exchange Molecular Dynamics Method for Protein Folding
-
Sugita, Y.; Okamoto, Y. Replica-Exchange Molecular Dynamics Method for Protein Folding Chem. Phys. Lett. 1999, 314, 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
74
-
-
36049031922
-
Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations
-
Kannan, S.; Zacharias, M. Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations Biophys. J. 2007, 93, 3218-3228
-
(2007)
Biophys. J.
, vol.93
, pp. 3218-3228
-
-
Kannan, S.1
Zacharias, M.2
-
75
-
-
77956602326
-
Exchange Often and Properly in Replica Exchange Molecular Dynamics
-
Sindhikara, D. J.; Emerson, D. J.; Roitberg, A. E. Exchange Often and Properly in Replica Exchange Molecular Dynamics J. Chem. Theory Comput. 2010, 6, 2804-2808
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2804-2808
-
-
Sindhikara, D.J.1
Emerson, D.J.2
Roitberg, A.E.3
-
76
-
-
33847201903
-
Exploring the Energy Landscape of Protein Folding Using Replica-Exchange and Conventional Molecular Dynamics Simulations
-
Beck, D. A. C.; White, G. W. N.; Daggett, V. Exploring the Energy Landscape of Protein Folding Using Replica-Exchange and Conventional Molecular Dynamics Simulations J. Struct. Biol. 2007, 157, 514-523
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 514-523
-
-
Beck, D.A.C.1
White, G.W.N.2
Daggett, V.3
-
77
-
-
33846106377
-
Convergence and Sampling Efficiency in Replica Exchange Simulations of Peptide Folding in Explicit Solvent
-
Periole, X.; Mark, A. E. Convergence and Sampling Efficiency in Replica Exchange Simulations of Peptide Folding in Explicit Solvent J. Chem. Phys. 2007, 126, 014903
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014903
-
-
Periole, X.1
Mark, A.E.2
-
78
-
-
66749128454
-
Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations
-
Rosta, E.; Buchete, N.-V.; Hummer, G. Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations J. Chem. Theory Comput. 2009, 5, 1393-1399
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1393-1399
-
-
Rosta, E.1
Buchete, N.-V.2
Hummer, G.3
-
79
-
-
0037157317
-
On the Hamiltonian Replica Exchange Method for Efficient Sampling of Biomolecular Systems: Application to Protein Structure Prediction
-
Fukunishi, H.; Watanabe, O.; Takada, S. On the Hamiltonian Replica Exchange Method for Efficient Sampling of Biomolecular Systems: Application to Protein Structure Prediction J. Chem. Phys. 2002, 116, 9058-9067
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 9058-9067
-
-
Fukunishi, H.1
Watanabe, O.2
Takada, S.3
-
80
-
-
33646203664
-
A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling
-
Affentranger, R.; Tavernelli, I.; Di Iorio, E. E. A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling J. Chem. Theory Comput. 2006, 2, 217-228
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 217-228
-
-
Affentranger, R.1
Tavernelli, I.2
Di Iorio, E.E.3
-
81
-
-
25444481354
-
Replica Exchange with Solute Tempering: A Method for Sampling Biological Systems in Explicit Water
-
Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J. Replica Exchange with Solute Tempering: A Method for Sampling Biological Systems in Explicit Water Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13749-13754
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 13749-13754
-
-
Liu, P.1
Kim, B.2
Friesner, R.A.3
Berne, B.J.4
-
82
-
-
33846227108
-
Enhanced Sampling of Peptide and Protein Conformations Using Replica Exchange Simulations with a Peptide Backbone Biasing-Potential
-
Kannan, S.; Zacharias, M. Enhanced Sampling of Peptide and Protein Conformations Using Replica Exchange Simulations with a Peptide Backbone Biasing-Potential Proteins: Struct., Funct., Bioinf. 2007, 66, 697-706
-
(2007)
Proteins: Struct., Funct., Bioinf.
, vol.66
, pp. 697-706
-
-
Kannan, S.1
Zacharias, M.2
-
83
-
-
0034294024
-
Multidimensional Replica-Exchange Method for Free-Energy Calculations
-
Sugita, Y.; Kitao, A.; Okamoto, Y. Multidimensional Replica-Exchange Method for Free-Energy Calculations J. Chem. Phys. 2000, 113, 6042-6051
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
84
-
-
84901063728
-
QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H and MM Approaches
-
10.1021/ct500183w
-
Kruse, H.; Havrila, M.; Sponer, J. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H and MM Approaches J. Chem. Theory Comput. 2014, 10.1021/ct500183w
-
(2014)
J. Chem. Theory Comput.
-
-
Kruse, H.1
Havrila, M.2
Sponer, J.3
-
85
-
-
80054004071
-
Evaluation of DNA Force Fields in Implicit Solvation
-
Gaillard, T.; Case, D. A. Evaluation of DNA Force Fields in Implicit Solvation J. Chem. Theory Comput. 2011, 7, 3181-3198
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 3181-3198
-
-
Gaillard, T.1
Case, D.A.2
-
86
-
-
84875760613
-
Metadynamics
-
Barducci, A.; Bonomi, M.; Parrinello, M. Metadynamics Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 826-843
-
(2011)
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
, vol.1
, pp. 826-843
-
-
Barducci, A.1
Bonomi, M.2
Parrinello, M.3
-
87
-
-
84881521091
-
Structural Dynamics of Possible Late-Stage Intermediates in Folding of Quadruplex DNA Studied by Molecular Simulations
-
Stadlbauer, P.; Krepl, M.; Cheatham, T. E.; Koca, J.; Sponer, J. Structural Dynamics of Possible Late-Stage Intermediates in Folding of Quadruplex DNA Studied by Molecular Simulations Nucleic Acids Res. 2013, 41, 7128-7143
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 7128-7143
-
-
Stadlbauer, P.1
Krepl, M.2
Cheatham, T.E.3
Koca, J.4
Sponer, J.5
-
88
-
-
84869008079
-
Free-Energy Landscape of a Thrombin-Binding DNA Aptamer in Aqueous Environment
-
Kim, E.; Yang, C.; Pak, Y. Free-Energy Landscape of a Thrombin-Binding DNA Aptamer in Aqueous Environment J. Chem. Theory Comput. 2012, 8, 4845-4851
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 4845-4851
-
-
Kim, E.1
Yang, C.2
Pak, Y.3
-
89
-
-
84873917136
-
The G-Triplex DNA
-
Limongelli, V.; De Tito, S.; Cerofolini, L.; Fragai, M.; Pagano, B.; Trotta, R.; Cosconati, S.; Marinelli, L.; Novellino, E.; Bertini, I.; Randazzo, A.; Luchinat, C.; Parrinello, M. The G-Triplex DNA Angew. Chem., Int. Ed. 2013, 52, 2269-2273
-
(2013)
Angew. Chem., Int. Ed.
, vol.52
, pp. 2269-2273
-
-
Limongelli, V.1
De Tito, S.2
Cerofolini, L.3
Fragai, M.4
Pagano, B.5
Trotta, R.6
Cosconati, S.7
Marinelli, L.8
Novellino, E.9
Bertini, I.10
Randazzo, A.11
Luchinat, C.12
Parrinello, M.13
-
90
-
-
0042823487
-
Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates
-
Stefl, R.; Cheatham, T. E.; Spackova, N.; Fadrna, E.; Berger, I.; Koca, J.; Sponer, J. Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates Biophys. J. 2003, 85, 1787-1804
-
(2003)
Biophys. J.
, vol.85
, pp. 1787-1804
-
-
Stefl, R.1
Cheatham, T.E.2
Spackova, N.3
Fadrna, E.4
Berger, I.5
Koca, J.6
Sponer, J.7
-
91
-
-
22144496413
-
Does Water Play a Structural Role in the Folding of Small Nucleic Acids?
-
Sorin, E. J.; Rhee, Y. M.; Pande, V. S. Does Water Play a Structural Role in the Folding of Small Nucleic Acids? Biophys. J. 2005, 88, 2516-2524
-
(2005)
Biophys. J.
, vol.88
, pp. 2516-2524
-
-
Sorin, E.J.1
Rhee, Y.M.2
Pande, V.S.3
-
92
-
-
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.; 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
-
(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
-
93
-
-
0032922174
-
A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat
-
Cheatham, T. E.; Cieplak, P.; Kollman, P. A. A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat J. Biomol. Struct. Dyn. 1999, 16, 845-862
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 845-862
-
-
Cheatham, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
94
-
-
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. Comput. Chem. 2000, 21, 1049-1074
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.M.1
Cieplak, P.2
Kollman, P.A.3
-
95
-
-
0000965687
-
Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations
-
Hobza, P.; Sponer, J. Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations Chem. Rev. 1999, 99, 3247-3276
-
(1999)
Chem. Rev.
, vol.99
, pp. 3247-3276
-
-
Hobza, P.1
Sponer, J.2
-
96
-
-
65249175089
-
Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the2 ′-OH Group of Ribose
-
Sponer, J.; Zgarbova, M.; Jurecka, P.; Riley, K. E.; Sponer, J. E.; Hobza, P. Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the2 ′-OH Group of Ribose J. Chem. Theory Comput. 2009, 5, 1166-1179
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1166-1179
-
-
Sponer, J.1
Zgarbova, M.2
Jurecka, P.3
Riley, K.E.4
Sponer, J.E.5
Hobza, P.6
-
97
-
-
84900474707
-
All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model
-
10.1002/jcc.23611
-
Savelyev, A.; MacKerell, A. D. All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model J. Comput. Chem. 2014, 10.1002/jcc.23611
-
(2014)
J. Comput. Chem.
-
-
Savelyev, A.1
MacKerell, A.D.2
-
98
-
-
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.; Orozco, M. Refinenement of the AMBER Force Field for Nucleic Acids: Improving the Description of Alpha/Gamma Conformers Biophys. J. 2007, 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
-
99
-
-
77952368283
-
Reparameterization of RNA π Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine
-
Yildirim, I.; Stern, H. A.; Kennedy, S. D.; Tubbs, J. D.; Turner, D. H. Reparameterization of RNA π Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine J. Chem. Theory Comput. 2010, 6, 1520-1531
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1520-1531
-
-
Yildirim, I.1
Stern, H.A.2
Kennedy, S.D.3
Tubbs, J.D.4
Turner, D.H.5
-
100
-
-
84872151052
-
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer
-
Drsata, T.; Perez, A.; Orozco, M.; Morozov, A. V.; Sponer, J.; Lankas, F. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer J. Chem. Theory Comput. 2013, 9, 707-721
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 707-721
-
-
Drsata, T.1
Perez, A.2
Orozco, M.3
Morozov, A.V.4
Sponer, J.5
Lankas, F.6
-
101
-
-
84882643757
-
CHARMM36 All-Atom Additive Protein Force Field: Validation Based on Comparison to NMR Data
-
Huang, J.; MacKerell, A. D. CHARMM36 All-Atom Additive Protein Force Field: Validation Based on Comparison to NMR Data J. Comput. Chem. 2013, 34, 2135-2145
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 2135-2145
-
-
Huang, J.1
MacKerell, A.D.2
-
102
-
-
84855656902
-
Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs
-
Yildirim, I.; Kennedy, S. D.; Stern, H. A.; Hart, J. M.; Kierzek, R.; Turner, D. H. Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs J. Chem. Theory Comput. 2011, 8, 172-181
-
(2011)
J. Chem. Theory Comput.
, vol.8
, pp. 172-181
-
-
Yildirim, I.1
Kennedy, S.D.2
Stern, H.A.3
Hart, J.M.4
Kierzek, R.5
Turner, D.H.6
-
103
-
-
0348244547
-
All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data
-
Foloppe, N.; MacKerell, A. D. All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data J. Comput. Chem. 2000, 21, 86-104
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell, A.D.2
-
104
-
-
49449085241
-
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
-
Joung, I. S.; Cheatham, T. E. Determination of Alkali and Halide Monovalent Ion Parameters for Use In Explicitly Solvated Biomolecular Simulations J. Phys. Chem. B 2008, 112, 9020-9041
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
105
-
-
84865231710
-
Structure and Mechanism of Purine-Binding Riboswitches
-
Batey, R. T. Structure and Mechanism of Purine-Binding Riboswitches Q. Rev. Biophys. 2012, 45, 345-381
-
(2012)
Q. Rev. Biophys.
, vol.45
, pp. 345-381
-
-
Batey, R.T.1
-
107
-
-
32244445917
-
Exploring the Energy Landscape of a Small RNA Hairpin
-
Ma, H.; Proctor, D. J.; Kierzek, E.; Kierzek, R.; Bevilacqua, P. C.; Gruebele, M. Exploring the Energy Landscape of a Small RNA Hairpin J. Am. Chem. Soc. 2006, 128, 1523-1530
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 1523-1530
-
-
Ma, H.1
Proctor, D.J.2
Kierzek, E.3
Kierzek, R.4
Bevilacqua, P.C.5
Gruebele, M.6
-
108
-
-
40149085374
-
Extending the NMR Spatial Resolution Limit for RNA by Motional Couplings
-
Zhang, Q.; Al-Hashimi, H. M. Extending the NMR Spatial Resolution Limit for RNA by Motional Couplings Nat. Methods 2008, 5, 243-245
-
(2008)
Nat. Methods
, vol.5
, pp. 243-245
-
-
Zhang, Q.1
Al-Hashimi, H.M.2
-
109
-
-
42449155819
-
RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics
-
Chen, S.-J. RNA Folding: Conformational Statistics, Folding Kinetics, and Ion Electrostatics Annu. Rev. Biophys. 2008, 37, 197-214
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 197-214
-
-
Chen, S.-J.1
-
110
-
-
79953060592
-
Cooperative and Directional Folding of the preQ1 Riboswitch Aptamer Domain
-
Feng, J.; Walter, N. G.; Brooks, C. L. Cooperative and Directional Folding of the preQ1 Riboswitch Aptamer Domain J. Am. Chem. Soc. 2011, 133, 4196-4199
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 4196-4199
-
-
Feng, J.1
Walter, N.G.2
Brooks, C.L.3
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