-
1
-
-
84946837767
-
-
John Wiley & Sons, Ltd: Chichester
-
Strauch, M. A. In eLS; John Wiley & Sons, Ltd: Chichester, 2001.
-
(2001)
eLS
-
-
Strauch, M.A.1
-
2
-
-
0035930331
-
Recognition of Specific DNA Sequences
-
Garvie, C. W.; Wolberger, C. Recognition of Specific DNA Sequences Mol. Cell 2001, 8, 937-946 10.1016/S1097-2765(01)00392-6
-
(2001)
Mol. Cell
, vol.8
, pp. 937-946
-
-
Garvie, C.W.1
Wolberger, C.2
-
3
-
-
84877031756
-
How Do Proteins Locate Specific Targets in DNA?
-
Redding, S.; Greene, E. C. How Do Proteins Locate Specific Targets in DNA? Chem. Phys. Lett. 2013, 570, 1-11 10.1016/j.cplett.2013.03.035
-
(2013)
Chem. Phys. Lett.
, vol.570
, pp. 1-11
-
-
Redding, S.1
Greene, E.C.2
-
4
-
-
51249090299
-
Importance of Accurate DNA Structures in Solution: The Jun-Fos Model
-
Heddi, B.; Foloppe, N.; Oguey, C.; Hartmann, B. Importance of Accurate DNA Structures in Solution: The Jun-Fos Model J. Mol. Biol. 2008, 382, 956-970 10.1016/j.jmb.2008.07.047
-
(2008)
J. Mol. Biol.
, vol.382
, pp. 956-970
-
-
Heddi, B.1
Foloppe, N.2
Oguey, C.3
Hartmann, B.4
-
5
-
-
34250318638
-
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
-
Perez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers Biophys. J. 2007, 92, 3817-3829 10.1529/biophysj.106.097782
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Perez, A.1
Marchán, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
6
-
-
49149093021
-
Geometrical and Electronic Structure Variability of the Sugar-Phosphate Backbone in Nucleic Acids
-
Svozil, D.; Šponer, J. E.; Marchan, I.; Pérez, A.; Cheatham, T. E., III; Forti, F.; Luque, F. J.; Orozco, M.; Šponer, J. Geometrical and Electronic Structure Variability of the Sugar-Phosphate Backbone in Nucleic Acids J. Phys. Chem. B 2008, 112, 8188-8197 10.1021/jp801245h
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 8188-8197
-
-
Svozil, D.1
Šponer, J.E.2
Marchan, I.3
Pérez, A.4
Cheatham, T.E.5
Forti, F.6
Luque, F.J.7
Orozco, M.8
Šponer, J.9
-
7
-
-
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., III; 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
-
8
-
-
84860767348
-
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
-
Götz, A. W.; Williamson, M. J.; Xu, D.; Poole, D.; Le Grand, S.; Walker, R. C. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born J. Chem. Theory Comput. 2012, 8, 1542-1555 10.1021/ct200909j
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1542-1555
-
-
Götz, A.W.1
Williamson, M.J.2
Xu, D.3
Poole, D.4
Le Grand, S.5
Walker, R.C.6
-
9
-
-
84923133278
-
On the Absence of Intrahelical DNA Dynamics on the us to ms Timescale
-
Galindo-Murillo, R.; Roe, D. R.; Cheatham, T. E., III On the Absence of Intrahelical DNA Dynamics on the us to ms Timescale Nat. Commun. 2014, 5, 5152 10.1038/ncomms6152
-
(2014)
Nat. Commun.
, vol.5
, pp. 5152
-
-
Galindo-Murillo, R.1
Roe, D.R.2
Cheatham, T.E.3
-
10
-
-
84923206685
-
Convergence and Reproducibility in Molecular Dynamics Simulations of the DNA Duplex d(GCACGAACGAACGAACGC)
-
Galindo-Murillo, R.; Roe, D. R.; Cheatham, T. E., III Convergence and Reproducibility in Molecular Dynamics Simulations of the DNA Duplex d(GCACGAACGAACGAACGC) Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 1041-1058 10.1016/j.bbagen.2014.09.007
-
(2015)
Biochim. Biophys. Acta, Gen. Subj.
, vol.1850
, pp. 1041-1058
-
-
Galindo-Murillo, R.1
Roe, D.R.2
Cheatham, T.E.3
-
11
-
-
84884192184
-
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
-
Salomon-Ferrer, R.; Götz, 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 10.1021/ct400314y
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3878-3888
-
-
Salomon-Ferrer, R.1
Götz, A.W.2
Poole, D.3
Le Grand, S.4
Walker, R.C.5
-
12
-
-
84899026778
-
Bioinformatic Analysis of the Protein/DNA Interface
-
Schneider, B.; Cerny, J.; Svozil, D.; Cech, P.; Gelly, J. C.; de Brevern, A. G. Bioinformatic Analysis of the Protein/DNA Interface Nucleic Acids Res. 2014, 42, 3381-3394 10.1093/nar/gkt1273
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 3381-3394
-
-
Schneider, B.1
Cerny, J.2
Svozil, D.3
Cech, P.4
Gelly, J.C.5
De Brevern, A.G.6
-
13
-
-
1242314385
-
DNA Fine Structure and Dynamics in Crystals and in Solution: The Impact of BI/BII Backbone Conformations
-
Djuranovic, D.; Hartmann, B. DNA Fine Structure and Dynamics in Crystals and in Solution: The Impact of BI/BII Backbone Conformations Biopolymers 2004, 73, 356-368 10.1002/bip.10528
-
(2004)
Biopolymers
, vol.73
, pp. 356-368
-
-
Djuranovic, D.1
Hartmann, B.2
-
14
-
-
0027335758
-
BI - BII Transitions in B-DNA
-
Hartmann, B.; Piazzola, D.; Lavery, R. BI-BII Transitions in B-DNA Nucleic Acids Res. 1993, 21, 561-568 10.1093/nar/21.3.561
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 561-568
-
-
Hartmann, B.1
Piazzola, D.2
Lavery, R.3
-
15
-
-
33746074088
-
Quantification of DNA BI/BII Backbone States in Solution. Implications for DNA Overall Structure and Recognition
-
Heddi, B.; Foloppe, N.; Bouchemal, N.; Hantz, E.; Hartmann, B. Quantification of DNA BI/BII Backbone States in Solution. Implications for DNA Overall Structure and Recognition J. Am. Chem. Soc. 2006, 128, 9170-9177 10.1021/ja061686j
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 9170-9177
-
-
Heddi, B.1
Foloppe, N.2
Bouchemal, N.3
Hantz, E.4
Hartmann, B.5
-
16
-
-
1442263634
-
Dynamics of DNA: BI and BII Phosphate Backbone Transitions
-
Trieb, M.; Rauch, C.; Wellenzohn, B.; Wibowo, F.; Loerting, T.; Liedl, K. R. Dynamics of DNA: BI and BII Phosphate Backbone Transitions J. Phys. Chem. B 2004, 108, 2470-2476 10.1021/jp037079p
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 2470-2476
-
-
Trieb, M.1
Rauch, C.2
Wellenzohn, B.3
Wibowo, F.4
Loerting, T.5
Liedl, K.R.6
-
17
-
-
0038118496
-
Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states
-
Djuranovic, D.; Hartmann, B. Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states J. Biomol. Struct. Dyn. 2003, 20, 771-788 10.1080/07391102.2003.10506894
-
(2003)
J. Biomol. Struct. Dyn.
, vol.20
, pp. 771-788
-
-
Djuranovic, D.1
Hartmann, B.2
-
18
-
-
0023350241
-
Nucleic Acid Model Building: The Multiple Backbone Solutions Associated with a Given Base Morphology
-
Srinivasan, A. R.; Olson, W. K. Nucleic Acid Model Building: The Multiple Backbone Solutions Associated with a Given Base Morphology J. Biomol. Struct. Dyn. 1987, 4, 895-938 10.1080/07391102.1987.10507690
-
(1987)
J. Biomol. Struct. Dyn.
, vol.4
, pp. 895-938
-
-
Srinivasan, A.R.1
Olson, W.K.2
-
19
-
-
0034624091
-
BII Nucleotides in the B and C Forms of Natural-sequence Polymeric DNA: A New Model for the C Form of DNA
-
van Dam, L.; Levitt, M. H. BII Nucleotides in the B and C Forms of Natural-sequence Polymeric DNA: A New Model for the C Form of DNA J. Mol. Biol. 2000, 304, 541-561 10.1006/jmbi.2000.4194
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 541-561
-
-
Van Dam, L.1
Levitt, M.H.2
-
20
-
-
0032755536
-
Helix Morphology Changes in B-DNA Induced By Spontaneous BI ⇌ BII Substate Interconversion
-
Winger, R. H.; Liedl, K. R.; Pichler, A.; Hallbrucker, A.; Mayer, E. Helix Morphology Changes in B-DNA Induced By Spontaneous BI ⇌ BII Substate Interconversion J. Biomol. Struct. Dyn. 1999, 17, 223-235 10.1080/07391102.1999.10508355
-
(1999)
J. Biomol. Struct. Dyn.
, vol.17
, pp. 223-235
-
-
Winger, R.H.1
Liedl, K.R.2
Pichler, A.3
Hallbrucker, A.4
Mayer, E.5
-
21
-
-
0030984104
-
Sensitivity of NMR Internucleotide Distances to B-DNA Conformation: Underlying Mechanics
-
Lefebvre, A.; Fermandjian, S.; Hartmann, B. Sensitivity of NMR Internucleotide Distances to B-DNA Conformation: Underlying Mechanics Nucleic Acids Res. 1997, 25, 3855-3862 10.1093/nar/25.19.3855
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3855-3862
-
-
Lefebvre, A.1
Fermandjian, S.2
Hartmann, B.3
-
22
-
-
3142657230
-
Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes
-
Kalodimos, C. G.; Biris, N.; Bonvin, A. M.; Levandoski, M. M.; Guennuegues, M.; Boelens, R.; Kaptein, R. Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes Science 2004, 305, 386-389 10.1126/science.1097064
-
(2004)
Science
, vol.305
, pp. 386-389
-
-
Kalodimos, C.G.1
Biris, N.2
Bonvin, A.M.3
Levandoski, M.M.4
Guennuegues, M.5
Boelens, R.6
Kaptein, R.7
-
23
-
-
0032417684
-
Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets
-
Rozenberg, H.; Rabinovich, D.; Frolow, F.; Hegde, R. S.; Shakked, Z. Structural Code for DNA Recognition Revealed in Crystal Structures of Papillomavirus E2-DNA Targets Proc. Natl. Acad. Sci. U. S. A. 1998, 95, 15194-15199 10.1073/pnas.95.26.15194
-
(1998)
Proc. Natl. Acad. Sci. U. S. A.
, vol.95
, pp. 15194-15199
-
-
Rozenberg, H.1
Rabinovich, D.2
Frolow, F.3
Hegde, R.S.4
Shakked, Z.5
-
24
-
-
2942620218
-
Predicting Indirect Readout Effects in Protein-DNA Interactions
-
Zhang, Y.; Xi, Z.; Hegde, R. S.; Shakked, Z.; Crothers, D. M. Predicting Indirect Readout Effects in Protein-DNA Interactions Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 8337-8341 10.1073/pnas.0402319101
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, pp. 8337-8341
-
-
Zhang, Y.1
Xi, Z.2
Hegde, R.S.3
Shakked, Z.4
Crothers, D.M.5
-
25
-
-
84884354648
-
The Papillomavirus E2 Proteins
-
McBride, A. A. The Papillomavirus E2 Proteins Virology 2013, 445, 57-79 10.1016/j.virol.2013.06.006
-
(2013)
Virology
, vol.445
, pp. 57-79
-
-
McBride, A.A.1
-
26
-
-
79960861304
-
Evolutionary Variation of Papillomavirus E2 Protein and E2 Binding Sites
-
Rogers, A.; Waltke, M.; Angeletti, P. C. Evolutionary Variation of Papillomavirus E2 Protein and E2 Binding Sites Virol. J. 2011, 8, 379 10.1186/1743-422X-8-379
-
(2011)
Virol. J.
, vol.8
, pp. 379
-
-
Rogers, A.1
Waltke, M.2
Angeletti, P.C.3
-
27
-
-
0023178843
-
Bovine Papillomavirus E2 Trans-Activating Gene Product Binds to Specific Sites in Papillomavirus DNA
-
Androphy, E. J.; Lowy, D. R.; Schiller, J. T. Bovine Papillomavirus E2 Trans-Activating Gene Product Binds to Specific Sites in Papillomavirus DNA Nature 1987, 325, 70-73 10.1038/325070a0
-
(1987)
Nature
, vol.325
, pp. 70-73
-
-
Androphy, E.J.1
Lowy, D.R.2
Schiller, J.T.3
-
28
-
-
0036086459
-
The Papillomavirus E2 Proteins: Structure, Function, and Biology
-
Hegde, R. S. The Papillomavirus E2 Proteins: Structure, Function, and Biology Annu. Rev. Biophys. Biomol. Struct. 2002, 31, 343-360 10.1146/annurev.biophys.31.100901.142129
-
(2002)
Annu. Rev. Biophys. Biomol. Struct.
, vol.31
, pp. 343-360
-
-
Hegde, R.S.1
-
29
-
-
0023958472
-
The Specific DNA Recognition Sequence of the Bovine Papillomavirus E2 Protein is an E2-Dependent Enhancer
-
Hawley-Nelson, P.; Androphy, E. J.; Lowy, D. R.; Schiller, J. T. The Specific DNA Recognition Sequence of the Bovine Papillomavirus E2 Protein is an E2-Dependent Enhancer EMBO J. 1988, 7, 525-531
-
(1988)
EMBO J.
, vol.7
, pp. 525-531
-
-
Hawley-Nelson, P.1
Androphy, E.J.2
Lowy, D.R.3
Schiller, J.T.4
-
30
-
-
0026656038
-
Crystal Structure at 1.7 A of the Bovine Papillomavirus-1 E2 DNA-binding Domain Bound to its DNA Target
-
Hegde, R. S.; Grossman, S. R.; Laimins, L. A.; Sigler, P. B. Crystal Structure at 1.7 A of the Bovine Papillomavirus-1 E2 DNA-binding Domain Bound to its DNA Target Nature 1992, 359, 505-512 10.1038/359505a0
-
(1992)
Nature
, vol.359
, pp. 505-512
-
-
Hegde, R.S.1
Grossman, S.R.2
Laimins, L.A.3
Sigler, P.B.4
-
31
-
-
25844495843
-
Molecular Dynamics Studies on Free and Bound Targets of the Bovine Papillomavirus Type I E2 Protein: The Protein Binding Effect on DNA and the Recognition Mechanism
-
Djuranovic, D.; Hartmann, B. Molecular Dynamics Studies on Free and Bound Targets of the Bovine Papillomavirus Type I E2 Protein: The Protein Binding Effect on DNA and the Recognition Mechanism Biophys. J. 2005, 89, 2542-2551 10.1529/biophysj.104.057109
-
(2005)
Biophys. J.
, vol.89
, pp. 2542-2551
-
-
Djuranovic, D.1
Hartmann, B.2
-
32
-
-
51049122626
-
MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation
-
Falconi, M.; Oteri, F.; Eliseo, T.; Cicero, D. O.; Desideri, A. MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation Biophys. J. 2008, 95, 1108-1117 10.1529/biophysj.108.130849
-
(2008)
Biophys. J.
, vol.95
, pp. 1108-1117
-
-
Falconi, M.1
Oteri, F.2
Eliseo, T.3
Cicero, D.O.4
Desideri, A.5
-
33
-
-
84906260782
-
Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA
-
Zgarbová, M.; Otyepka, M.; Šponer, J.; Lankaš, F.; Jurečka, P. Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA J. Chem. Theory Comput. 2014, 10, 3177-3189 10.1021/ct500120v
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 3177-3189
-
-
Zgarbová, M.1
Otyepka, M.2
Šponer, J.3
Lankaš, F.4
Jurečka, P.5
-
34
-
-
84946893188
-
-
University of California, San Francisco: San Francisco, CA
-
Case, D. A.; Berryman, J. T.; Betz, R. M.; Cerutti, D. S.; T.E. Cheatham, I.; Darden, T. A.; Duke, R. E.; Giese, T. J.; Golke, H.; Goetz, A. W.; et al. AMBER 15; University of California, San Francisco: San Francisco, CA, 2015.
-
(2015)
AMBER 15
-
-
Case, D.A.1
Berryman, J.T.2
Betz, R.M.3
Cerutti, D.S.4
Cheatham, I.T.E.5
Darden, T.A.6
Duke, R.E.7
Giese, T.J.8
Golke, H.9
Goetz, A.W.10
-
35
-
-
80052820313
-
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
-
Zgarbová, M.; Otyepka, M.; Šponer, J.; Mládek, A.; Banáš, P.; Cheatham, T. E. I.; Jurečka, 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
-
-
Zgarbová, M.1
Otyepka, M.2
Šponer, J.3
Mládek, A.4
Banáš, P.5
Cheatham, T.E.I.6
Jurečka, P.7
-
36
-
-
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
-
37
-
-
49449085241
-
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
-
Joung, I. S.; Cheatham, T. E., III 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
-
38
-
-
84927779536
-
Long Time Step Molecular Dynamics through Hydrogen Mass Repartitioning
-
Hopkins, C. W.; Le Grand, S.; Walker, R. C.; Roitberg, A. E. Long Time Step Molecular Dynamics through Hydrogen Mass Repartitioning J. Chem. Theory Comput. 2015, 11, 1864-1874 10.1021/ct5010406
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 1864-1874
-
-
Hopkins, C.W.1
Le Grand, S.2
Walker, R.C.3
Roitberg, A.E.4
-
39
-
-
84904760980
-
-
University of California, San Francisco: San Francisco, CA
-
Case, D. A.; Babin, V.; Berryman, J. T.; Betz, R. M.; Cai, Q.; Cerutti, D. S.; Cheatham, T. E., III; Darden, T. A.; Duke, R. E.; Gohlke, H.; et al. AMBER 14; University of California, San Francisco: San Francisco, CA, 2014.
-
(2014)
AMBER 14
-
-
Case, D.A.1
Babin, V.2
Berryman, J.T.3
Betz, R.M.4
Cai, Q.5
Cerutti, D.S.6
Cheatham, T.E.7
Darden, T.A.8
Duke, R.E.9
Gohlke, H.10
-
40
-
-
33750587438
-
Molecular Dynamics with Coupling to an External Bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690 10.1063/1.448118
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
41
-
-
33646940952
-
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
-
Ryckaert, J. P. J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes J. Comput. Phys. 1977, 23, 327-341 10.1016/0021-9991(77)90098-5
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
42
-
-
84952104504
-
An Analysis of the Accuracy of Langevin and Molecular Dynamics Algorithms
-
Pastor, R. W.; Brooks, B. R.; Szabo, A. An Analysis of the Accuracy of Langevin and Molecular Dynamics Algorithms Mol. Phys. 1988, 65, 1409-1419 10.1080/00268978800101881
-
(1988)
Mol. Phys.
, vol.65
, pp. 1409-1419
-
-
Pastor, R.W.1
Brooks, B.R.2
Szabo, A.3
-
43
-
-
70450261721
-
Conformational Analysis of Nucleic Acids Revisited: Curves+
-
Lavery, R.; Moakher, M.; Maddocks, J. H.; Petkeviciute, D.; Zakrzewska, K. Conformational Analysis of Nucleic Acids Revisited: Curves+ Nucleic Acids Res. 2009, 37, 5917-5929 10.1093/nar/gkp608
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5917-5929
-
-
Lavery, R.1
Moakher, M.2
Maddocks, J.H.3
Petkeviciute, D.4
Zakrzewska, K.5
-
44
-
-
84880022273
-
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
-
Roe, D. R.; Cheatham, T. E., III PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data J. Chem. Theory Comput. 2013, 9, 3084-3095 10.1021/ct400341p
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3084-3095
-
-
Roe, D.R.1
Cheatham, T.E.2
-
45
-
-
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., III Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide J. Chem. Theory Comput. 2014, 10, 492-499 10.1021/ct400862k
-
(2014)
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
-
46
-
-
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
-
47
-
-
79957788878
-
ProDy: Protein Dynamics Inferred from Theory and Experiments
-
Bakan, A.; Meireles, L. M.; Bahar, I. ProDy: Protein Dynamics Inferred from Theory and Experiments Bioinformatics 2011, 27, 1575-1577 10.1093/bioinformatics/btr168
-
(2011)
Bioinformatics
, vol.27
, pp. 1575-1577
-
-
Bakan, A.1
Meireles, L.M.2
Bahar, I.3
-
48
-
-
20944449840
-
Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis
-
Madhumalar, A.; Bansal, M. Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis J. Biomol. Struct. Dyn. 2005, 23, 13-27 10.1080/07391102.2005.10507043
-
(2005)
J. Biomol. Struct. Dyn.
, vol.23
, pp. 13-27
-
-
Madhumalar, A.1
Bansal, M.2
|