-
1
-
-
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. 2010, 43, 40-47 10.1021/ar900093g
-
(2010)
Acc. Chem. Res.
, vol.43
, pp. 40-47
-
-
Ditzler, M.A.1
Otyepka, M.2
Sponer, J.3
Walter, N.G.4
-
2
-
-
84901047861
-
Molecular Dynamics Simulations of Nucleic Acids. from Tetranucleotides to the Ribosome
-
Sponer, J.; Banas, P.; Jurecka, P.; Zgarbova, M.; Kuhrova, P.; Havrila, M.; Krepl, M.; Stadlbauer, P.; Otyepka, M. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome J. Phys. Chem. Lett. 2014, 5, 1771-1782 10.1021/jz500557y
-
(2014)
J. Phys. Chem. Lett.
, vol.5
, pp. 1771-1782
-
-
Sponer, J.1
Banas, P.2
Jurecka, P.3
Zgarbova, M.4
Kuhrova, P.5
Havrila, M.6
Krepl, M.7
Stadlbauer, P.8
Otyepka, M.9
-
3
-
-
84884931806
-
Twenty-Five Years of Nucleic Acid Simulations
-
Cheatham, T. E.; Case, D. A. Twenty-Five Years of Nucleic Acid Simulations Biopolymers 2013, 99, 969-977 10.1002/bip.22331
-
(2013)
Biopolymers
, vol.99
, pp. 969-977
-
-
Cheatham, T.E.1
Case, D.A.2
-
4
-
-
84857033265
-
Atomistic Molecular Simulations of Protein Folding
-
Best, R. B. Atomistic Molecular Simulations of Protein Folding Curr. Opin. Struct. Biol. 2012, 22, 52-61 10.1016/j.sbi.2011.12.001
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 52-61
-
-
Best, R.B.1
-
5
-
-
77957572546
-
Challenges in Protein-Folding Simulations
-
Freddolino, P. L.; Harrison, C. B.; Liu, Y. X.; Schulten, K. Challenges in Protein-Folding Simulations Nat. Phys. 2010, 6, 751-758 10.1038/nphys1713
-
(2010)
Nat. Phys.
, vol.6
, pp. 751-758
-
-
Freddolino, P.L.1
Harrison, C.B.2
Liu, Y.X.3
Schulten, K.4
-
6
-
-
84935905798
-
Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering
-
Zhang, T.; Nguyen, P. H.; Nasica-Labouze, J.; Mu, Y. G.; Derreumaux, P. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering J. Phys. Chem. B 2015, 119, 6941-6951 10.1021/acs.jpcb.5b03381
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 6941-6951
-
-
Zhang, T.1
Nguyen, P.H.2
Nasica-Labouze, J.3
Mu, Y.G.4
Derreumaux, P.5
-
7
-
-
84960467661
-
Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems
-
Pan, A. C.; Weinreich, T. M.; Piana, S.; Shaw, D. E. Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems J. Chem. Theory Comput. 2016, 12, 1360-1367 10.1021/acs.jctc.5b00913
-
(2016)
J. Chem. Theory Comput.
, vol.12
, pp. 1360-1367
-
-
Pan, A.C.1
Weinreich, T.M.2
Piana, S.3
Shaw, D.E.4
-
8
-
-
84893173849
-
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
-
Abrams, C.; Bussi, G. Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration Entropy 2014, 16, 163-199 10.3390/e16010163
-
(2014)
Entropy
, vol.16
, pp. 163-199
-
-
Abrams, C.1
Bussi, G.2
-
9
-
-
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.; Otyepka, M. Theoretical Studies of RNA Catalysis: Hybrid Qm/Mm Methods and Their Comparison with Md and Qm Methods 2009, 49, 202-216 10.1016/j.ymeth.2009.04.007
-
(2009)
Methods
, vol.49
, pp. 202-216
-
-
Banas, P.1
Jurecka, P.2
Walter, N.G.3
Sponer, J.4
Otyepka, M.5
-
10
-
-
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 10.1016/S0009-2614(99)01123-9
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
11
-
-
79960928036
-
Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (Rest2)
-
Wang, L.; Friesner, R. A.; Berne, B. J. Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (Rest2) J. Phys. Chem. B 2011, 115, 11305-11305 10.1021/jp207931v
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 11305
-
-
Wang, L.1
Friesner, R.A.2
Berne, B.J.3
-
12
-
-
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 10.1073/pnas.0506346102
-
(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
-
13
-
-
38349091489
-
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
-
Barducci, A.; Bussi, G.; Parrinello, M. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method Phys. Rev. Lett. 2008, 100, 020603 10.1103/PhysRevLett.100.020603
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 020603
-
-
Barducci, A.1
Bussi, G.2
Parrinello, M.3
-
15
-
-
84875760613
-
Metadynamics
-
Barducci, A.; Bonomi, M.; Parrinello, M. Metadynamics Wires Comput. Mol. Sci. 2011, 1, 826-843 10.1002/wcms.31
-
(2011)
Wires Comput. Mol. Sci.
, vol.1
, pp. 826-843
-
-
Barducci, A.1
Bonomi, M.2
Parrinello, M.3
-
16
-
-
84973389250
-
-
John Wiley and Sons, Inc. Hoboken, NJ
-
Bussi, G.; Branduardi, D. Free-Energy Calculations with Metadynamics: Theory and Practice; John Wiley and Sons, Inc.: Hoboken, NJ, 2015; Vol. 28.
-
(2015)
Free-Energy Calculations with Metadynamics: Theory and Practice
, vol.28
-
-
Bussi, G.1
Branduardi, D.2
-
17
-
-
0029121733
-
Exceptionally Stable Nucleic-Acid Hairpins
-
Varani, G. Exceptionally Stable Nucleic-Acid Hairpins Annu. Rev. Biophys. Biomol. Struct. 1995, 24, 379-404 10.1146/annurev.bb.24.060195.002115
-
(1995)
Annu. Rev. Biophys. Biomol. Struct.
, vol.24
, pp. 379-404
-
-
Varani, G.1
-
18
-
-
0025061676
-
Nucleic-Acid Structure - Tetraloops and RNA Folding
-
Uhlenbeck, O. C. Nucleic-Acid Structure-Tetraloops and RNA Folding Nature 1990, 346, 613-614 10.1038/346613a0
-
(1990)
Nature
, vol.346
, pp. 613-614
-
-
Uhlenbeck, O.C.1
-
19
-
-
0028037302
-
Model for an RNA Tertiary Interaction Front the Structure of an Intermolecular Complex between a Gaaa Tetraloop and an RNA Helix
-
Pley, H. W.; Flaherty, K. M.; Mckay, D. B. Model for an RNA Tertiary Interaction Front the Structure of an Intermolecular Complex between a Gaaa Tetraloop and an RNA Helix Nature 1994, 372, 111-113 10.1038/372111a0
-
(1994)
Nature
, vol.372
, pp. 111-113
-
-
Pley, H.W.1
Flaherty, K.M.2
McKay, D.B.3
-
20
-
-
57049151833
-
Annotation of Tertiary Interactions in RNA Structures Reveals Variations and Correlations
-
Xin, Y. R.; Laing, C.; Leontis, N. B.; Schlick, T. Annotation of Tertiary Interactions in RNA Structures Reveals Variations and Correlations RNA 2008, 14, 2465-2477 10.1261/rna.1249208
-
(2008)
RNA
, vol.14
, pp. 2465-2477
-
-
Xin, Y.R.1
Laing, C.2
Leontis, N.B.3
Schlick, T.4
-
21
-
-
38649085954
-
Tertiary Interactions Determine the Accuracy of RNA Folding
-
Chauhan, S.; Woodson, S. A. Tertiary Interactions Determine the Accuracy of RNA Folding J. Am. Chem. Soc. 2008, 130, 1296-1303 10.1021/ja076166i
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 1296-1303
-
-
Chauhan, S.1
Woodson, S.A.2
-
22
-
-
0029001288
-
Bent Helix Formation between RNA Hairpins with Complementary Loops
-
Marino, J. P.; Gregorian, R. S.; Csankovszki, G.; Crothers, D. M. Bent Helix Formation between RNA Hairpins with Complementary Loops Science 1995, 268, 1448-1454 10.1126/science.7539549
-
(1995)
Science
, vol.268
, pp. 1448-1454
-
-
Marino, J.P.1
Gregorian, R.S.2
Csankovszki, G.3
Crothers, D.M.4
-
23
-
-
84922982407
-
Tetraloop-Like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides
-
Stadlbauer, P.; Sponer, J.; Costanzo, G.; Di Mauro, E.; Pino, S.; Sponer, J. E. Tetraloop-Like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides Chem.-Eur. J. 2015, 21, 3596-3604 10.1002/chem.201406140
-
(2015)
Chem. - Eur. J.
, vol.21
, pp. 3596-3604
-
-
Stadlbauer, P.1
Sponer, J.2
Costanzo, G.3
Di Mauro, E.4
Pino, S.5
Sponer, J.E.6
-
24
-
-
0028294458
-
Involvement of a Gnra Tetraloop in Long-Range Tertiary Interactions
-
Jaeger, L.; Michel, F.; Westhof, E. Involvement of a Gnra Tetraloop in Long-Range Tertiary Interactions J. Mol. Biol. 1994, 236, 1271-1276 10.1016/0022-2836(94)90055-8
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 1271-1276
-
-
Jaeger, L.1
Michel, F.2
Westhof, E.3
-
25
-
-
0031009237
-
Hierarchy and Dynamics of RNA Folding
-
Brion, P.; Westhof, E. Hierarchy and Dynamics of RNA Folding Annu. Rev. Biophys. Biomol. Struct. 1997, 26, 113-137 10.1146/annurev.biophys.26.1.113
-
(1997)
Annu. Rev. Biophys. Biomol. Struct.
, vol.26
, pp. 113-137
-
-
Brion, P.1
Westhof, E.2
-
26
-
-
0026593806
-
Thermodynamic Parameters for Loop Formation in RNA and DNA Hairpin Tetraloops
-
Antao, V. P.; Tinoco, I. Thermodynamic Parameters for Loop Formation in RNA and DNA Hairpin Tetraloops Nucleic Acids Res. 1992, 20, 819-824 10.1093/nar/20.4.819
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 819-824
-
-
Antao, V.P.1
Tinoco, I.2
-
27
-
-
0042845840
-
Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations
-
Sorin, E. J.; Rhee, Y. M.; Nakatani, B. J.; Pande, V. S. Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations Biophys. J. 2003, 85, 790-803 10.1016/S0006-3495(03)74520-2
-
(2003)
Biophys. J.
, vol.85
, pp. 790-803
-
-
Sorin, E.J.1
Rhee, Y.M.2
Nakatani, B.J.3
Pande, V.S.4
-
28
-
-
84920168531
-
Energy Landscapes, Folding Mechanisms, and Kinetics of RNA Tetraloop Hairpins
-
Chakraborty, D.; Collepardo-Guevara, R.; Wales, D. J. Energy Landscapes, Folding Mechanisms, and Kinetics of RNA Tetraloop Hairpins J. Am. Chem. Soc. 2014, 136, 18052-18061 10.1021/ja5100756
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 18052-18061
-
-
Chakraborty, D.1
Collepardo-Guevara, R.2
Wales, D.J.3
-
29
-
-
84875989318
-
Computer Folding of RNA Tetraloops? Are We There Yet?
-
Kuhrova, 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 10.1021/ct301086z
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2115-2125
-
-
Kuhrova, P.1
Banas, P.2
Best, R.B.3
Sponer, J.4
Otyepka, M.5
-
30
-
-
33645521068
-
Single Nucleotide RNA Choreography
-
Hsiao, C.; Mohan, S.; Hershkovitz, E.; Tannenbaum, A.; Williams, L. D. Single Nucleotide RNA Choreography Nucleic Acids Res. 2006, 34, 1481-1491 10.1093/nar/gkj500
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1481-1491
-
-
Hsiao, C.1
Mohan, S.2
Hershkovitz, E.3
Tannenbaum, A.4
Williams, L.D.5
-
31
-
-
84939177498
-
Insights into Stability and Folding of Gnra and Uncg Tetra Loops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics
-
Haldar, S.; Kuhrova, P.; Banas, P.; Spiwok, V.; Sponer, J.; Hobza, P.; Otyepka, M. Insights into Stability and Folding of Gnra and Uncg Tetra Loops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics J. Chem. Theory Comput. 2015, 11, 3866-3877 10.1021/acs.jctc.5b00010
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 3866-3877
-
-
Haldar, S.1
Kuhrova, P.2
Banas, P.3
Spiwok, V.4
Sponer, J.5
Hobza, P.6
Otyepka, M.7
-
32
-
-
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 10.1021/ct100481h
-
(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
-
33
-
-
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 10.1073/pnas.1309392110
-
(2013)
Proc. Natl. Acad. Sci. U. S. A.
, vol.110
, pp. 16820-16825
-
-
Chen, A.A.1
Garcia, A.E.2
-
34
-
-
84925265010
-
Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with Epsilon/Zeta Force Field Reparametrizations
-
Mlynsky, V.; Kuhrova, P.; Zgarbova, M.; Jurecka, P.; Walter, N. G.; Otyepka, M.; Sponer, J.; Banas, P. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with Epsilon/Zeta Force Field Reparametrizations J. Phys. Chem. B 2015, 119, 4220-4229 10.1021/jp512069n
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 4220-4229
-
-
Mlynsky, V.1
Kuhrova, P.2
Zgarbova, M.3
Jurecka, P.4
Walter, N.G.5
Otyepka, M.6
Sponer, J.7
Banas, P.8
-
35
-
-
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 10.1529/biophysj.106.097782
-
(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
-
36
-
-
77952368283
-
Reparameterization of RNA Chi 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 Chi Torsion Parameters for the Amber Force Field and Comparison to Nmr Spectra for Cytidine and Uridine J. Chem. Theory Comput. 2010, 6, 1520-1531 10.1021/ct900604a
-
(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
-
37
-
-
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., 3rd; 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 10.1021/ct400154j
-
(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
-
38
-
-
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 10.1021/ct200162x
-
(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
-
39
-
-
84865723813
-
Optimization of the Additive Charmm All-Atom Protein Force Field Targeting Improved Sampling of the Backbone Phi, Psi and Side-Chain Chi(1) and Chi(2) Dihedral Angles
-
Best, R. B.; Zhu, X.; Shim, J.; Lopes, P. E. M.; Mittal, J.; Feig, M.; MacKerell, A. D. Optimization of the Additive Charmm All-Atom Protein Force Field Targeting Improved Sampling of the Backbone Phi, Psi and Side-Chain Chi(1) and Chi(2) Dihedral Angles J. Chem. Theory Comput. 2012, 8, 3257-3273 10.1021/ct300400x
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3257-3273
-
-
Best, R.B.1
Zhu, X.2
Shim, J.3
Lopes, P.E.M.4
Mittal, J.5
Feig, M.6
MacKerell, A.D.7
-
40
-
-
84867761593
-
Simulations of a-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration
-
Besseova, I.; Banas, P.; Kuhrova, 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 10.1021/jp3014817
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 9899-9916
-
-
Besseova, I.1
Banas, P.2
Kuhrova, P.3
Kosinova, P.4
Otyepka, M.5
Sponer, J.6
-
41
-
-
84867801144
-
Molecular Mechanism of Preq(1) Riboswitch Action: A Molecular Dynamics Study
-
Banas, P.; Sklenovsky, P.; Wedekind, J. E.; Sponer, J.; Otyepka, M. Molecular Mechanism of Preq(1) Riboswitch Action: A Molecular Dynamics Study J. Phys. Chem. B 2012, 116, 12721-12734 10.1021/jp309230v
-
(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
-
42
-
-
0001216964
-
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. 1996, 118, 2309-2309 10.1021/ja955032e
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 2309
-
-
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
-
43
-
-
84900474707
-
All- Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model
-
Savelyev, A.; MacKerell, A. D. All- Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model J. Comput. Chem. 2014, 35, 1219-1239 10.1002/jcc.23611
-
(2014)
J. Comput. Chem.
, vol.35
, pp. 1219-1239
-
-
Savelyev, A.1
MacKerell, A.D.2
-
44
-
-
84892572123
-
Are Waters around RNA More Than Just a Solvent? - An Insight from Molecular Dynamics Simulations
-
Kuehrova, P.; Otyepka, M.; Sponer, J.; Banas, P. Are Waters around RNA More Than Just a Solvent?-an Insight from Molecular Dynamics Simulations J. Chem. Theory Comput. 2014, 10, 401-411 10.1021/ct400663s
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 401-411
-
-
Kuehrova, P.1
Otyepka, M.2
Sponer, J.3
Banas, P.4
-
45
-
-
77952472539
-
Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38h(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme
-
Mlynsky, V.; Banas, P.; Hollas, D.; Reblova, K.; Walter, N. G.; Sponer, J.; Otyepka, M. Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38h(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme J. Phys. Chem. B 2010, 114, 6642-6652 10.1021/jp1001258
-
(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
-
46
-
-
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. 2012, 8, 172-181 10.1021/ct200557r
-
(2012)
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
-
47
-
-
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 10.1039/c2cp41987d
-
(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
-
48
-
-
84869065540
-
Revised Amber Parameters for Bioorganic Phosphates
-
Steinbrecher, T.; Latzer, J.; Case, D. A. Revised Amber Parameters for Bioorganic Phosphates J. Chem. Theory Comput. 2012, 8, 4405-4412 10.1021/ct300613v
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 4405-4412
-
-
Steinbrecher, T.1
Latzer, J.2
Case, D.A.3
-
49
-
-
84941041808
-
Improved Force Field Parameters Lead to a Better Description of RNA Structure
-
Bergonzo, C.; Cheatham, T. E. Improved Force Field Parameters Lead to a Better Description of RNA Structure J. Chem. Theory Comput. 2015, 11, 3969-3972 10.1021/acs.jctc.5b00444
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 3969-3972
-
-
Bergonzo, C.1
Cheatham, T.E.2
-
50
-
-
84863686749
-
Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics
-
Banas, P.; Mladek, A.; Otyepka, M.; Zgarbova, M.; Jurecka, P.; Svozil, D.; Lankas, F.; Sponer, J. Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics J. Chem. Theory Comput. 2012, 8, 2448-2460 10.1021/ct3001238
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2448-2460
-
-
Banas, P.1
Mladek, A.2
Otyepka, M.3
Zgarbova, M.4
Jurecka, P.5
Svozil, D.6
Lankas, F.7
Sponer, J.8
-
51
-
-
84949656411
-
Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 Mus Explicit-Solvent Molecular Dynamics Simulations
-
Schrodt, M. V.; Andrews, C. T.; Elcock, A. H. Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 Mus Explicit-Solvent Molecular Dynamics Simulations J. Chem. Theory Comput. 2015, 11, 5906-5917 10.1021/acs.jctc.5b00899
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 5906-5917
-
-
Schrodt, M.V.1
Andrews, C.T.2
Elcock, A.H.3
-
52
-
-
84939789620
-
Highly Sampled Tetranucleotide and Tetraloop Motifs Enable Evaluation of Common RNA Force Fields
-
Bergonzo, C.; Henriksen, N. M.; Roe, D. R.; Cheatham, T. E., 3rd Highly Sampled Tetranucleotide and Tetraloop Motifs Enable Evaluation of Common RNA Force Fields RNA 2015, 21, 1578-1590 10.1261/rna.051102.115
-
(2015)
RNA
, vol.21
, pp. 1578-1590
-
-
Bergonzo, C.1
Henriksen, N.M.2
Roe, D.R.3
Cheatham, T.E.4
-
53
-
-
84949604777
-
Microsecond-Scale Md Simulations of HIV-1 Dis Kissing-Loop Complexes Predict Bulged-in Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the Amber RNA Force Fields
-
Havrila, M.; Zgarbova, M.; Jurecka, P.; Banas, P.; Krepl, M.; Otyepka, M.; Sponer, J. Microsecond-Scale Md Simulations of Hiv-1 Dis Kissing-Loop Complexes Predict Bulged-in Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the Amber RNA Force Fields J. Phys. Chem. B 2015, 119, 15176-15190 10.1021/acs.jpcb.5b08876
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 15176-15190
-
-
Havrila, M.1
Zgarbova, M.2
Jurecka, P.3
Banas, P.4
Krepl, M.5
Otyepka, M.6
Sponer, J.7
-
54
-
-
70549103338
-
Dependence of a-RNA Simulations on the Choice of the Force Field and Salt Strength
-
Besseova, I.; Otyepka, M.; Reblova, K.; Sponer, J. Dependence of a-RNA Simulations on the Choice of the Force Field and Salt Strength Phys. Chem. Chem. Phys. 2009, 11, 10701-10711 10.1039/b911169g
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 10701-10711
-
-
Besseova, I.1
Otyepka, M.2
Reblova, K.3
Sponer, J.4
-
55
-
-
84944239723
-
Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit
-
Kruse, H.; Mladek, A.; Gkionis, K.; Hansen, A.; Grimme, S.; Sponer, J. Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit J. Chem. Theory Comput. 2015, 11, 4972-4991 10.1021/acs.jctc.5b00515
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 4972-4991
-
-
Kruse, H.1
Mladek, A.2
Gkionis, K.3
Hansen, A.4
Grimme, S.5
Sponer, J.6
-
56
-
-
0345531092
-
The Common and the Distinctive Features of the Bulged-G Motif Based on a 1.04 Angstrom Resolution RNA Structure
-
Correll, C. C.; Beneken, J.; Plantinga, M. J.; Lubbers, M.; Chan, Y. L. The Common and the Distinctive Features of the Bulged-G Motif Based on a 1.04 Angstrom Resolution RNA Structure Nucleic Acids Res. 2003, 31, 6806-6818 10.1093/nar/gkg908
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6806-6818
-
-
Correll, C.C.1
Beneken, J.2
Plantinga, M.J.3
Lubbers, M.4
Chan, Y.L.5
-
57
-
-
69849114530
-
Classification and Energetics of the Base-Phosphate Interactions in RNA
-
Zirbel, C. L.; Sponer, J. E.; Sponer, J.; Stombaugh, J.; Leontis, N. B. Classification and Energetics of the Base-Phosphate Interactions in RNA Nucleic Acids Res. 2009, 37, 4898-4918 10.1093/nar/gkp468
-
(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
-
58
-
-
84873719639
-
An Overview of the Amber Biomolecular Simulation Package
-
Salomon-Ferrer, R.; Case, D. A.; Walker, R. C. An Overview of the Amber Biomolecular Simulation Package Wires Comput. Mol. Sci. 2013, 3, 198-210 10.1002/wcms.1121
-
(2013)
Wires Comput. Mol. Sci.
, vol.3
, pp. 198-210
-
-
Salomon-Ferrer, R.1
Case, D.A.2
Walker, R.C.3
-
59
-
-
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 10.1063/1.445869
-
(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
-
60
-
-
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 10.1021/jp8001614
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
61
-
-
35948987540
-
Parameters of Monovalent Ions in the Amber-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements
-
Chen, A. A.; Pappu, R. V. Parameters of Monovalent Ions in the Amber-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements J. Phys. Chem. B 2007, 111, 11884-11887 10.1021/jp0765392
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 11884-11887
-
-
Chen, A.A.1
Pappu, R.V.2
-
62
-
-
0344796204
-
Ion Water Interaction Potentials Derived from Free-Energy Perturbation Simulations
-
Aqvist, J. Ion Water Interaction Potentials Derived from Free-Energy Perturbation Simulations J. Phys. Chem. 1990, 94, 8021-8024 10.1021/j100384a009
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8021-8024
-
-
Aqvist, J.1
-
63
-
-
0035010211
-
Geometric Nomenclature and Classification of RNA Base Pairs
-
Leontis, N. B.; Westhof, E. Geometric Nomenclature and Classification of RNA Base Pairs RNA 2001, 7, 499-512 10.1017/S1355838201002515
-
(2001)
RNA
, vol.7
, pp. 499-512
-
-
Leontis, N.B.1
Westhof, E.2
-
64
-
-
46249092554
-
Gromacs 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. Gromacs 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447 10.1021/ct700301q
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
65
-
-
69349100797
-
Plumed: A Portable Plugin for Free-Energy Calculations with Molecular Dynamics
-
Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A.; Parrinello, M. Plumed: A Portable Plugin for Free-Energy Calculations with Molecular Dynamics Comput. Phys. Commun. 2009, 180, 1961-1972 10.1016/j.cpc.2009.05.011
-
(2009)
Comput. Phys. Commun.
, vol.180
, pp. 1961-1972
-
-
Bonomi, M.1
Branduardi, D.2
Bussi, G.3
Camilloni, C.4
Provasi, D.5
Raiteri, P.6
Donadio, D.7
Marinelli, F.8
Pietrucci, F.9
Broglia, R.A.10
Parrinello, M.11
-
66
-
-
4043137165
-
Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs
-
Sponer, J.; Jurecka, P.; Hobza, P. Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs J. Am. Chem. Soc. 2004, 126, 10142-10151 10.1021/ja048436s
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 10142-10151
-
-
Sponer, J.1
Jurecka, P.2
Hobza, P.3
-
67
-
-
0029878720
-
Vmd: Visual Molecular Dynamics
-
Humphrey, W.; Dalke, A.; Schulten, K. Vmd: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38 10.1016/0263-7855(96)00018-5
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
68
-
-
84885059377
-
A Simple Bootstrap Method for Constructing Nonparametric Confidence Bands for Functions
-
Hall, P.; Horowitz, J. A Simple Bootstrap Method for Constructing Nonparametric Confidence Bands for Functions Ann. Stat 2013, 41, 1892-1921 10.1214/13-AOS1137
-
(2013)
Ann. Stat
, vol.41
, pp. 1892-1921
-
-
Hall, P.1
Horowitz, J.2
-
69
-
-
77956890307
-
On Blocking Rules for the Bootstrap with Dependent Data
-
Hall, P.; Horowitz, J. L.; Jing, B. Y. On Blocking Rules for the Bootstrap with Dependent Data Biometrika 1995, 82, 561-574 10.1093/biomet/82.3.561
-
(1995)
Biometrika
, vol.82
, pp. 561-574
-
-
Hall, P.1
Horowitz, J.L.2
Jing, B.Y.3
-
70
-
-
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., 3rd 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 10.1021/jp400530e
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 4014-4027
-
-
Henriksen, N.M.1
Roe, D.R.2
Cheatham, T.E.3
-
71
-
-
0034681945
-
Dynamics of the RNA Hairpin Gnra Tetraloop
-
Menger, M.; Eckstein, F.; Porschke, D. Dynamics of the RNA Hairpin Gnra Tetraloop Biochemistry 2000, 39, 4500-4507 10.1021/bi992297n
-
(2000)
Biochemistry
, vol.39
, pp. 4500-4507
-
-
Menger, M.1
Eckstein, F.2
Porschke, D.3
-
72
-
-
34247159140
-
Direct Revelation of Multiple Conformations in RNA by Femtosecond Dynamics
-
Zhao, L.; Xia, T. B. Direct Revelation of Multiple Conformations in RNA by Femtosecond Dynamics J. Am. Chem. Soc. 2007, 129, 4118-4119 10.1021/ja068391q
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 4118-4119
-
-
Zhao, L.1
Xia, T.B.2
-
73
-
-
84941094198
-
The Role of Nucleobase Interactions in RNA Structure and Dynamics
-
Bottaro, S.; Di Palma, F.; Bussi, G. The Role of Nucleobase Interactions in RNA Structure and Dynamics Nucleic Acids Res. 2014, 42, 13306-13314 10.1093/nar/gku972
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 13306-13314
-
-
Bottaro, S.1
Di Palma, F.2
Bussi, G.3
-
74
-
-
84903289127
-
Clustering by Fast Search and Find of Density Peaks
-
Rodriguez, A.; Laio, A. Clustering by Fast Search and Find of Density Peaks Science 2014, 344, 1492-1496 10.1126/science.1242072
-
(2014)
Science
, vol.344
, pp. 1492-1496
-
-
Rodriguez, A.1
Laio, A.2
-
75
-
-
38349110269
-
Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin
-
Garcia, A. E.; Paschek, D. Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin J. Am. Chem. Soc. 2008, 130, 815-817 10.1021/ja074191i
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 815-817
-
-
Garcia, A.E.1
Paschek, D.2
-
76
-
-
0026423027
-
Structural Features That Give Rise to the Unusual Stability of RNA Hairpins Containing Gnra Loops
-
Heus, H. A.; Pardi, A. Structural Features That Give Rise to the Unusual Stability of RNA Hairpins Containing Gnra Loops Science 1991, 253, 191-194 10.1126/science.1712983
-
(1991)
Science
, vol.253
, pp. 191-194
-
-
Heus, H.A.1
Pardi, A.2
-
77
-
-
0027749314
-
High-Resolution Nmr-Study of a Synthetic Oligoribonucleotide with a Tetranucleotide Gaga Loop That Is a Substrate for the Cytotoxic Protein, Ricin
-
Orita, M.; Nishikawa, F.; Shimayama, T.; Taira, K.; Endo, Y.; Nishikawa, S. High-Resolution Nmr-Study of a Synthetic Oligoribonucleotide with a Tetranucleotide Gaga Loop That Is a Substrate for the Cytotoxic Protein, Ricin Nucleic Acids Res. 1993, 21, 5670-5678 10.1093/nar/21.24.5670
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 5670-5678
-
-
Orita, M.1
Nishikawa, F.2
Shimayama, T.3
Taira, K.4
Endo, Y.5
Nishikawa, S.6
-
78
-
-
62549095901
-
A Fast Selenium Derivatization Strategy for Crystallization and Phasing of RNA Structures
-
Olieric, V.; Rieder, U.; Lang, K.; Serganov, A.; Schulze-Briese, C.; Micura, R.; Dumas, P.; Ennifar, E. A Fast Selenium Derivatization Strategy for Crystallization and Phasing of RNA Structures RNA 2009, 15, 707-715 10.1261/rna.1499309
-
(2009)
RNA
, vol.15
, pp. 707-715
-
-
Olieric, V.1
Rieder, U.2
Lang, K.3
Serganov, A.4
Schulze-Briese, C.5
Micura, R.6
Dumas, P.7
Ennifar, E.8
-
79
-
-
84916625049
-
An Introduction to Recurrent Nucleotide Interactions in RNA
-
Sweeney, B. A.; Roy, P.; Leontis, N. B. An Introduction to Recurrent Nucleotide Interactions in RNA Wiley Interdiscip Rev: RNA 2015, 6, 17-45 10.1002/wrna.1258
-
(2015)
Wiley Interdiscip Rev: RNA
, vol.6
, pp. 17-45
-
-
Sweeney, B.A.1
Roy, P.2
Leontis, N.B.3
-
80
-
-
33744807172
-
The Building Blocks and Motifs of RNA Architecture
-
Leontis, N. B.; Lescoute, A.; Westhof, E. The Building Blocks and Motifs of RNA Architecture Curr. Opin. Struct. Biol. 2006, 16, 279-287 10.1016/j.sbi.2006.05.009
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 279-287
-
-
Leontis, N.B.1
Lescoute, A.2
Westhof, E.3
-
81
-
-
36448954303
-
Fr3d: Finding Local and Composite Recurrent Structural Motifs in RNA 3d Structures
-
Sarver, M.; Zirbel, C. L.; Stombaugh, J.; Mokdad, A.; Leontis, N. B. Fr3d: Finding Local and Composite Recurrent Structural Motifs in RNA 3d Structures J. Math Biol. 2007, 56, 215-252 10.1007/s00285-007-0110-x
-
(2007)
J. Math Biol.
, vol.56
, pp. 215-252
-
-
Sarver, M.1
Zirbel, C.L.2
Stombaugh, J.3
Mokdad, A.4
Leontis, N.B.5
-
82
-
-
70349594633
-
Fast Folding of an RNA Tetraloop on a Rugged Energy Landscape Detected by a Stacking-Sensitive Probe
-
Sarkar, K.; Meister, K.; Sethi, A.; Gruebele, M. Fast Folding of an RNA Tetraloop on a Rugged Energy Landscape Detected by a Stacking-Sensitive Probe Biophys. J. 2009, 97, 1418-1427 10.1016/j.bpj.2009.06.035
-
(2009)
Biophys. J.
, vol.97
, pp. 1418-1427
-
-
Sarkar, K.1
Meister, K.2
Sethi, A.3
Gruebele, M.4
-
83
-
-
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 10.1021/ja0553856
-
(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
-
84
-
-
2442626706
-
Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure
-
Mathews, D. H.; Disney, M. D.; Childs, J. L.; Schroeder, S. J.; Zuker, M.; Turner, D. H. Incorporating Chemical Modification Constraints into a Dynamic Programming Algorithm for Prediction of RNA Secondary Structure Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 7287-7292 10.1073/pnas.0401799101
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 7287-7292
-
-
Mathews, D.H.1
Disney, M.D.2
Childs, J.L.3
Schroeder, S.J.4
Zuker, M.5
Turner, D.H.6
-
85
-
-
84864917111
-
Non-Specific Binding of Na+ and Mg2+ to RNA Determined by Force Spectroscopy Methods
-
Bizarro, C. V.; Alemany, A.; Ritort, F. Non-Specific Binding of Na+ and Mg2+ to RNA Determined by Force Spectroscopy Methods Nucleic Acids Res. 2012, 40, 6922-6935 10.1093/nar/gks289
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 6922-6935
-
-
Bizarro, C.V.1
Alemany, A.2
Ritort, F.3
-
86
-
-
0043289936
-
Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5 ′-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA
-
Gresh, N.; Sponer, J. E.; Spackova, N.; Leszczynski, J.; Sponer, J. Theoretical Study of Binding of Hydrated Zn(Ii) and Mg(Ii) Cations to 5 ′-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA J. Phys. Chem. B 2003, 107, 8669-8681 10.1021/jp022659s
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 8669-8681
-
-
Gresh, N.1
Sponer, J.E.2
Spackova, N.3
Leszczynski, J.4
Sponer, J.5
-
87
-
-
84946866716
-
Charge Screening in RNA: An Integral Route for Dynamical Enhancements
-
Roh, J. H.; Tyagi, M.; Aich, P.; Kim, K.; Briber, R. M.; Woodson, S. A. Charge Screening in RNA: An Integral Route for Dynamical Enhancements Soft Matter 2015, 11, 8741-8745 10.1039/C5SM02084K
-
(2015)
Soft Matter
, vol.11
, pp. 8741-8745
-
-
Roh, J.H.1
Tyagi, M.2
Aich, P.3
Kim, K.4
Briber, R.M.5
Woodson, S.A.6
-
88
-
-
32244445917
-
Exploring the Energy Landscape of a Small RNA Hairpin
-
Ma, H. R.; 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 10.1021/ja0553856
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 1523-1530
-
-
Ma, H.R.1
Proctor, D.J.2
Kierzek, E.3
Kierzek, R.4
Bevilacqua, P.C.5
Gruebele, M.6
-
89
-
-
40449091092
-
RNA Backbone: Consensus All-Angle Conformers and Modular String Nomenclature (an RNA Ontology Consortium Contribution)
-
Richardson, J. S.; Schneider, B.; Murray, L. W.; Kapral, G. J.; Immormino, R. M.; Headd, J. J.; Richardson, D. C.; Ham, D.; Hershkovits, E.; Williams, L. D.; Keating, K. S.; Pyle, A. M.; Micallef, D.; Westbrook, J.; Berman, H. M. RNA Backbone: Consensus All-Angle Conformers and Modular String Nomenclature (an RNA Ontology Consortium Contribution) RNA 2008, 14, 465-481 10.1261/rna.657708
-
(2008)
RNA
, vol.14
, pp. 465-481
-
-
Richardson, J.S.1
Schneider, B.2
Murray, L.W.3
Kapral, G.J.4
Immormino, R.M.5
Headd, J.J.6
Richardson, D.C.7
Ham, D.8
Hershkovits, E.9
Williams, L.D.10
Keating, K.S.11
Pyle, A.M.12
Micallef, D.13
Westbrook, J.14
Berman, H.M.15
-
90
-
-
79960650298
-
Benchmarking Amber Force Fields for RNA: Comparisons to Nmr Spectra for Single-Stranded R(Gacc) Are Improved by Revised Chi 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 Chi Torsions J. Phys. Chem. B 2011, 115, 9261-9270 10.1021/jp2016006
-
(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
-
91
-
-
84931265187
-
Stacking in RNA: Nmr of Four Tetramers Benchmark Molecular Dynamics
-
Condon, D. E.; Kennedy, S. D.; Mort, B. C.; Kierzek, R.; Yildirim, I.; Turner, D. H. Stacking in RNA: Nmr of Four Tetramers Benchmark Molecular Dynamics J. Chem. Theory Comput. 2015, 11, 2729-2742 10.1021/ct501025q
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 2729-2742
-
-
Condon, D.E.1
Kennedy, S.D.2
Mort, B.C.3
Kierzek, R.4
Yildirim, I.5
Turner, D.H.6
-
92
-
-
65249175089
-
Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2 ′-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 the 2 ′-Oh Group of Ribose J. Chem. Theory Comput. 2009, 5, 1166-1179 10.1021/ct800547k
-
(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
-
93
-
-
84929164515
-
Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised Amber Parameters and Compared with Experiment
-
Brown, R. F.; Andrews, C. T.; Elcock, A. H. Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised Amber Parameters and Compared with Experiment J. Chem. Theory Comput. 2015, 11, 2315-2328 10.1021/ct501170h
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 2315-2328
-
-
Brown, R.F.1
Andrews, C.T.2
Elcock, A.H.3
-
94
-
-
84944790300
-
Molecular Mechanism for Preq1-II Riboswitch Function Revealed by Molecular Dynamics
-
Aytenfisu, A. H.; Liberman, J. A.; Wedekind, J. E.; Mathews, D. H. Molecular Mechanism for Preq1-Ii Riboswitch Function Revealed by Molecular Dynamics RNA 2015, 21, 1898-907 10.1261/rna.051367.115
-
(2015)
RNA
, vol.21
, pp. 1898-1907
-
-
Aytenfisu, A.H.1
Liberman, J.A.2
Wedekind, J.E.3
Mathews, D.H.4
-
95
-
-
84936136220
-
Structural Analysis of a Class III Preq1 Riboswitch Reveals an Aptamer Distant from a Ribosome-Binding Site Regulated by Fast Dynamics
-
Liberman, J. A.; Suddala, K. C.; Aytenfisu, A.; Chan, D.; Belashov, I. A.; Salim, M.; Mathews, D. H.; Spitale, R. C.; Walter, N. G.; Wedekind, J. E. Structural Analysis of a Class Iii Preq1 Riboswitch Reveals an Aptamer Distant from a Ribosome-Binding Site Regulated by Fast Dynamics Proc. Natl. Acad. Sci. U. S. A. 2015, 112, E3485-E3494 10.1073/pnas.1503955112
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, pp. E3485-E3494
-
-
Liberman, J.A.1
Suddala, K.C.2
Aytenfisu, A.3
Chan, D.4
Belashov, I.A.5
Salim, M.6
Mathews, D.H.7
Spitale, R.C.8
Walter, N.G.9
Wedekind, J.E.10
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