-
1
-
-
84884931806
-
Twenty five years of nucleic acid simulations
-
Cheatham, T. E.; Case, D. A. Twenty five years of nucleic acid simulations Biopolymers 2013, 99 (12) 969-977 10.1002/bip.22331
-
(2013)
Biopolymers
, vol.99
, Issue.12
, pp. 969-977
-
-
Cheatham, T.E.1
Case, D.A.2
-
2
-
-
33846823909
-
Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98 (12) 10089-10092 10.1063/1.464397
-
(1993)
J. Chem. Phys.
, vol.98
, Issue.12
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
3
-
-
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 (19) 5179-5197 10.1021/ja00124a002
-
(1995)
J. Am. Chem. Soc.
, vol.117
, Issue.19
, 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
-
4
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang, J.; 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 (12) 1049-1074 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F
-
(2000)
J. Comput. Chem.
, vol.21
, Issue.12
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
5
-
-
0029170114
-
Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
-
Cheatham, T. E., III; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins J. Am. Chem. Soc. 1995, 117 (14) 4193-4194 10.1021/ja00119a045
-
(1995)
J. Am. Chem. Soc.
, vol.117
, Issue.14
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
6
-
-
36749098380
-
Dynamics of B-DNA on the Microsecond Time Scale
-
Pérez, A.; Luque, F. J.; Orozco, M. Dynamics of B-DNA on the Microsecond Time Scale J. Am. Chem. Soc. 2007, 129 (47) 14739-14745 10.1021/ja0753546
-
(2007)
J. Am. Chem. Soc.
, vol.129
, Issue.47
, pp. 14739-14745
-
-
Pérez, A.1
Luque, F.J.2
Orozco, M.3
-
7
-
-
84923206685
-
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)
-
Galindo-Murillo, R.; Roe, D. R.; Cheatham, T. E. Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC) Biochim. Biophys. Acta, Gen. Subj. 2015, 1850 (5) 1041-1058 10.1016/j.bbagen.2014.09.007
-
(2015)
Biochim. Biophys. Acta, Gen. Subj.
, vol.1850
, Issue.5
, pp. 1041-1058
-
-
Galindo-Murillo, R.1
Roe, D.R.2
Cheatham, T.E.3
-
8
-
-
34250318638
-
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
-
Pérez, 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 (11) 3817-3829 10.1529/biophysj.106.097782
-
(2007)
Biophys. J.
, vol.92
, Issue.11
, pp. 3817-3829
-
-
Pérez, A.1
Marchán, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
9
-
-
78651294111
-
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
-
Banáš, P.; Hollas, D.; Zgarbová, M.; Jurečka, P.; Orozco, M.; Cheatham, T. E.; Šponer, J. i.; Otyepka, M. Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins J. Chem. Theory Comput. 2010, 6 (12) 3836-3849 10.1021/ct100481h
-
(2010)
J. Chem. Theory Comput.
, vol.6
, Issue.12
, pp. 3836-3849
-
-
Banáš, P.1
Hollas, D.2
Zgarbová, M.3
Jurečka, P.4
Orozco, M.5
Cheatham, T.E.6
Šponer, J.I.7
Otyepka, M.8
-
10
-
-
84923151437
-
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
-
Pasi, M.; Maddocks, J. H.; Beveridge, D.; Bishop, T. C.; Case, D. A.; Cheatham, T.; Dans, P. D.; Jayaram, B.; Lankas, F.; Laughton, C.; Mitchell, J.; Osman, R.; Orozco, M.; Pérez, A.; Petkevičiute, D.; Spackova, N.; Sponer, J.; Zakrzewska, K.; Lavery, R. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA Nucleic Acids Res. 2014, 42 (19) 12272-12283 10.1093/nar/gku855
-
(2014)
Nucleic Acids Res.
, vol.42
, Issue.19
, pp. 12272-12283
-
-
Pasi, M.1
Maddocks, J.H.2
Beveridge, D.3
Bishop, T.C.4
Case, D.A.5
Cheatham, T.6
Dans, P.D.7
Jayaram, B.8
Lankas, F.9
Laughton, C.10
Mitchell, J.11
Osman, R.12
Orozco, M.13
Pérez, A.14
Petkevičiute, D.15
Spackova, N.16
Sponer, J.17
Zakrzewska, K.18
Lavery, R.19
-
11
-
-
33750035856
-
Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model
-
Okur, A.; Wickstrom, L.; Layten, M.; Geney, R.; Song, K.; Hornak, V.; Simmerling, C. Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model J. Chem. Theory Comput. 2006, 2 (2) 420-433 10.1021/ct050196z
-
(2006)
J. Chem. Theory Comput.
, vol.2
, Issue.2
, pp. 420-433
-
-
Okur, A.1
Wickstrom, L.2
Layten, M.3
Geney, R.4
Song, K.5
Hornak, V.6
Simmerling, C.7
-
12
-
-
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 (1-2) 141-151 10.1016/S0009-2614(99)01123-9
-
(1999)
Chem. Phys. Lett.
, vol.314
, Issue.1-2
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
13
-
-
0042561888
-
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
-
Zagrovic, B.; Pande, V. Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study J. Comput. Chem. 2003, 24 (12) 1432-1436 10.1002/jcc.10297
-
(2003)
J. Comput. Chem.
, vol.24
, Issue.12
, pp. 1432-1436
-
-
Zagrovic, B.1
Pande, V.2
-
14
-
-
0034701222
-
Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model
-
Tsui, V.; Case, D. A. Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model J. Am. Chem. Soc. 2000, 122 (11) 2489-2498 10.1021/ja9939385
-
(2000)
J. Am. Chem. Soc.
, vol.122
, Issue.11
, pp. 2489-2498
-
-
Tsui, V.1
Case, D.A.2
-
15
-
-
64649105762
-
Accelerating molecular dynamic simulation on graphics processing units
-
Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. Accelerating molecular dynamic simulation on graphics processing units J. Comput. Chem. 2009, 30 (6) 864-872 10.1002/jcc.21209
-
(2009)
J. Comput. Chem.
, vol.30
, Issue.6
, pp. 864-872
-
-
Friedrichs, M.S.1
Eastman, P.2
Vaidyanathan, V.3
Houston, M.4
Legrand, S.5
Beberg, A.L.6
Ensign, D.L.7
Bruns, C.M.8
Pande, V.S.9
-
16
-
-
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 (5) 1542-1555 10.1021/ct200909j
-
(2012)
J. Chem. Theory Comput.
, vol.8
, Issue.5
, 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
-
17
-
-
33846783019
-
Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study
-
Graf, J.; Nguyen, P. H.; Stock, G.; Schwalbe, H. Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study J. Am. Chem. Soc. 2007, 129 (5) 1179-1189 10.1021/ja0660406
-
(2007)
J. Am. Chem. Soc.
, vol.129
, Issue.5
, pp. 1179-1189
-
-
Graf, J.1
Nguyen, P.H.2
Stock, G.3
Schwalbe, H.4
-
18
-
-
84907943526
-
Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent
-
Nguyen, H.; Maier, J.; Huang, H.; Perrone, V.; Simmerling, C. Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent J. Am. Chem. Soc. 2014, 136 (40) 13959-13962 10.1021/ja5032776
-
(2014)
J. Am. Chem. Soc.
, vol.136
, Issue.40
, pp. 13959-13962
-
-
Nguyen, H.1
Maier, J.2
Huang, H.3
Perrone, V.4
Simmerling, C.5
-
19
-
-
33749259954
-
Kinking occurs during molecular dynamics simulations of small DNA minicircles
-
Lankas, F.; Lavery, R.; Maddocks, J. H. Kinking occurs during molecular dynamics simulations of small DNA minicircles Structure 2006, 14 (10) 1527-1534 10.1016/j.str.2006.08.004
-
(2006)
Structure
, vol.14
, Issue.10
, pp. 1527-1534
-
-
Lankas, F.1
Lavery, R.2
Maddocks, J.H.3
-
20
-
-
79956013643
-
Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA
-
Mitchell, J. S.; Laughton, C. A.; Harris, S. A. Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA Nucleic Acids Res. 2011, 39 (9) 3928-3938 10.1093/nar/gkq1312
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.9
, pp. 3928-3938
-
-
Mitchell, J.S.1
Laughton, C.A.2
Harris, S.A.3
-
21
-
-
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 (10) 3181-3198 10.1021/ct200384r
-
(2011)
J. Chem. Theory Comput.
, vol.7
, Issue.10
, pp. 3181-3198
-
-
Gaillard, T.1
Case, D.A.2
-
22
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 1983, 4 (2) 187-217 10.1002/jcc.540040211
-
(1983)
J. Comput. Chem.
, vol.4
, Issue.2
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
23
-
-
0037157693
-
Novel generalized Born methods
-
Lee, M. S.; Salsbury, F. R.; Brooks, C. L. Novel generalized Born methods J. Chem. Phys. 2002, 116 (24) 10606-10614 10.1063/1.1480013
-
(2002)
J. Chem. Phys.
, vol.116
, Issue.24
, pp. 10606-10614
-
-
Lee, M.S.1
Salsbury, F.R.2
Brooks, C.L.3
-
24
-
-
0038792211
-
New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations
-
Lee, M. S.; Feig, M.; Salsbury, F. R.; Brooks, C. L. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations J. Comput. Chem. 2003, 24 (11) 1348-1356 10.1002/jcc.10272
-
(2003)
J. Comput. Chem.
, vol.24
, Issue.11
, pp. 1348-1356
-
-
Lee, M.S.1
Feig, M.2
Salsbury, F.R.3
Brooks, C.L.4
-
25
-
-
0141956090
-
Generalized born model with a simple smoothing function
-
Im, W.; Lee, M. S.; Brooks, C. L. Generalized born model with a simple smoothing function J. Comput. Chem. 2003, 24 (14) 1691-1702 10.1002/jcc.10321
-
(2003)
J. Comput. Chem.
, vol.24
, Issue.14
, pp. 1691-1702
-
-
Im, W.1
Lee, M.S.2
Brooks, C.L.3
-
26
-
-
0002636134
-
Pairwise solute descreening of solute charges from a dielectric medium
-
Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Pairwise solute descreening of solute charges from a dielectric medium Chem. Phys. Lett. 1995, 246 (1-2) 122-129 10.1016/0009-2614(95)01082-K
-
(1995)
Chem. Phys. Lett.
, vol.246
, Issue.1-2
, pp. 122-129
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
27
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model Proteins: Struct., Funct., Genet. 2004, 55 (2) 383-394 10.1002/prot.20033
-
(2004)
Proteins: Struct., Funct., Genet.
, vol.55
, Issue.2
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
28
-
-
58049201323
-
-
University of California: San Francisco
-
Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 10; University of California: San Francisco, 2008.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossvary, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
29
-
-
84862614975
-
-
University of California: San Francisco
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Goetz, A. W.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 12; University of California: San Francisco, 2012.
-
(2012)
AMBER 12
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.11
Hayik, S.12
Roitberg, A.13
Seabra, G.14
Swails, J.15
Goetz, A.W.16
Kolossváry, I.17
Wong, K.F.18
Paesani, F.19
Vanicek, J.20
Wolf, R.M.21
Liu, J.22
Wu, X.23
Brozell, S.R.24
Steinbrecher, T.25
Gohlke, H.26
Cai, Q.27
Ye, X.28
Wang, J.29
Hsieh, M.-J.30
Cui, G.31
Roe, D.R.32
Mathews, D.H.33
Seetin, M.G.34
Salomon-Ferrer, R.35
Sagui, C.36
Babin, V.37
Luchko, T.38
Gusarov, S.39
Kovalenko, A.40
Kollman, P.A.41
more..
-
30
-
-
84904760980
-
-
University of California: San Francisco
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Goetz, A. W.; I. Kolossváry; Wong, K. F.; Paesani, F.; Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 14; University of California: San Francisco, 2014.
-
(2014)
AMBER 14
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.11
Hayik, S.12
Roitberg, A.13
Seabra, G.14
Swails, J.15
Goetz, A.W.16
Kolossváry, I.17
Wong, K.F.18
Paesani, F.19
Vanicek, J.20
Wolf, R.M.21
Liu, J.22
Wu, X.23
Brozell, S.R.24
Steinbrecher, T.25
Gohlke, H.26
Cai, Q.27
Ye, X.28
Wang, J.29
Hsieh, M.-J.30
Cui, G.31
Roe, D.R.32
Mathews, D.H.33
Seetin, M.G.34
Salomon-Ferrer, R.35
Sagui, C.36
Babin, V.37
Luchko, T.38
Gusarov, S.39
Kovalenko, A.40
Kollman, P.A.41
more..
-
31
-
-
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 10.1021/ct200384r
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 3181-3198
-
-
Gaillard, T.1
Case, D.A.2
-
32
-
-
0032560959
-
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices
-
Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices J. Am. Chem. Soc. 1998, 120 (37) 9401-9409 10.1021/ja981844+
-
(1998)
J. Am. Chem. Soc.
, vol.120
, Issue.37
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
33
-
-
14244273182
-
Theory and applications of the generalized born solvation model in macromolecular simulations
-
Tsui, V.; Case, D. A. Theory and applications of the generalized born solvation model in macromolecular simulations Biopolymers 2000, 56 (4) 275-291 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E
-
(2000)
Biopolymers
, vol.56
, Issue.4
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
34
-
-
33845365528
-
A Computational Study of Nucleosomal DNA Flexibility
-
Ruscio, J. Z.; Onufriev, A. A Computational Study of Nucleosomal DNA Flexibility Biophys. J. 2006, 91 (11) 4121-4132 10.1529/biophysj.106.082099
-
(2006)
Biophys. J.
, vol.91
, Issue.11
, pp. 4121-4132
-
-
Ruscio, J.Z.1
Onufriev, A.2
-
35
-
-
1642419747
-
Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches
-
Cheng, X.; Hornak, V.; Simmerling, C. Improved Conformational Sampling through an Efficient Combination of Mean-Field Simulation Approaches J. Phys. Chem. B 2004, 108 (1) 426-437 10.1021/jp034505y
-
(2004)
J. Phys. Chem. B
, vol.108
, Issue.1
, pp. 426-437
-
-
Cheng, X.1
Hornak, V.2
Simmerling, C.3
-
36
-
-
0037120830
-
Conformational Heterogeneity Observed in Simulations of a Pyrene-Substituted DNA
-
Cui, G.; Simmerling, C. Conformational Heterogeneity Observed in Simulations of a Pyrene-Substituted DNA J. Am. Chem. Soc. 2002, 124 (41) 12154-12164 10.1021/ja026825l
-
(2002)
J. Am. Chem. Soc.
, vol.124
, Issue.41
, pp. 12154-12164
-
-
Cui, G.1
Simmerling, C.2
-
37
-
-
18544381108
-
Modified Replica Exchange Simulation Methods for Local Structure Refinement
-
Cheng, X.; Cui, G.; Hornak, V.; Simmerling, C. Modified Replica Exchange Simulation Methods for Local Structure Refinement J. Phys. Chem. B 2005, 109 (16) 8220-8230 10.1021/jp045437y
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.16
, pp. 8220-8230
-
-
Cheng, X.1
Cui, G.2
Hornak, V.3
Simmerling, C.4
-
38
-
-
0033064123
-
Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model
-
Williams, D. J.; Hall, K. B. Unrestrained Stochastic Dynamics Simulations of the UUCG Tetraloop Using an Implicit Solvation Model Biophys. J. 1999, 76 (6) 3192-3205 10.1016/S0006-3495(99)77471-0
-
(1999)
Biophys. J.
, vol.76
, Issue.6
, pp. 3192-3205
-
-
Williams, D.J.1
Hall, K.B.2
-
39
-
-
0345731284
-
Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations
-
Hall, K. B.; Williams, D. J. Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations RNA 2004, 10 (1) 34-47 10.1261/rna.5133404
-
(2004)
RNA
, vol.10
, Issue.1
, pp. 34-47
-
-
Hall, K.B.1
Williams, D.J.2
-
40
-
-
84988087911
-
Calculating the electrostatic potential of molecules in solution: Method and error assessment
-
Gilson, M. K.; Sharp, K. A.; Honig, B. H. Calculating the electrostatic potential of molecules in solution: Method and error assessment J. Comput. Chem. 1988, 9 (4) 327-335 10.1002/jcc.540090407
-
(1988)
J. Comput. Chem.
, vol.9
, Issue.4
, pp. 327-335
-
-
Gilson, M.K.1
Sharp, K.A.2
Honig, B.H.3
-
41
-
-
0346971105
-
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Charles, L.; Brooks, I. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures J. Comput. Chem. 2004, 25 (2) 265-284 10.1002/jcc.10378
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.2
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Charles, L.6
Brooks, I.7
-
42
-
-
33645703426
-
Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations
-
Chocholoušová, J.; Feig, M. Balancing an accurate representation of the molecular surface in generalized born formalisms with integrator stability in molecular dynamics simulations J. Comput. Chem. 2006, 27 (6) 719-729 10.1002/jcc.20387
-
(2006)
J. Comput. Chem.
, vol.27
, Issue.6
, pp. 719-729
-
-
Chocholoušová, J.1
Feig, M.2
-
43
-
-
0001585978
-
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
-
Feenstra, K. A.; Hess, B.; Berendsen, H. J. C. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems J. Comput. Chem. 1999, 20 (8) 786-798 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.3.CO;2-2
-
(1999)
J. Comput. Chem.
, vol.20
, Issue.8
, pp. 786-798
-
-
Feenstra, K.A.1
Hess, B.2
Berendsen, H.J.C.3
-
44
-
-
33847723384
-
Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation
-
Roe, D. R.; Okur, A.; Wickstrom, L.; Hornak, V.; Simmerling, C. Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation J. Phys. Chem. B 2007, 111 (7) 1846-1857 10.1021/jp066831u
-
(2007)
J. Phys. Chem. B
, vol.111
, Issue.7
, pp. 1846-1857
-
-
Roe, D.R.1
Okur, A.2
Wickstrom, L.3
Hornak, V.4
Simmerling, C.5
-
45
-
-
33847713183
-
Generalized Born Model with a Simple, Robust Molecular Volume Correction
-
Mongan, J.; Simmerling, C.; McCammon, J. A.; Case, D. A.; Onufriev, A. Generalized Born Model with a Simple, Robust Molecular Volume Correction J. Chem. Theory Comput. 2007, 3 (1) 156-169 10.1021/ct600085e
-
(2007)
J. Chem. Theory Comput.
, vol.3
, Issue.1
, pp. 156-169
-
-
Mongan, J.1
Simmerling, C.2
McCammon, J.A.3
Case, D.A.4
Onufriev, A.5
-
46
-
-
46749105987
-
A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation
-
Shell, M. S.; Ritterson, R.; Dill, K. A. A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation J. Phys. Chem. B 2008, 112 (22) 6878-6886 10.1021/jp800282x
-
(2008)
J. Phys. Chem. B
, vol.112
, Issue.22
, pp. 6878-6886
-
-
Shell, M.S.1
Ritterson, R.2
Dill, K.A.3
-
47
-
-
84875983100
-
Improved Generalized Born Solvent Model Parameters for Protein Simulations
-
Nguyen, H.; Roe, D. R.; Simmerling, C. Improved Generalized Born Solvent Model Parameters for Protein Simulations J. Chem. Theory Comput. 2013, 9 (4) 2020-2034 10.1021/ct3010485
-
(2013)
J. Chem. Theory Comput.
, vol.9
, Issue.4
, pp. 2020-2034
-
-
Nguyen, H.1
Roe, D.R.2
Simmerling, C.3
-
48
-
-
84873526912
-
To milliseconds and beyond: challenges in the simulation of protein folding
-
Lane, T. J.; Shukla, D.; Beauchamp, K. A.; Pande, V. S. To milliseconds and beyond: challenges in the simulation of protein folding Curr. Opin. Struct. Biol. 2013, 23 (1) 58-65 10.1016/j.sbi.2012.11.002
-
(2013)
Curr. Opin. Struct. Biol.
, vol.23
, Issue.1
, pp. 58-65
-
-
Lane, T.J.1
Shukla, D.2
Beauchamp, K.A.3
Pande, V.S.4
-
49
-
-
42049087036
-
Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions
-
Chen, J.; Brooks, C. L. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions Phys. Chem. Chem. Phys. 2008, 10 (4) 471-481 10.1039/B714141F
-
(2008)
Phys. Chem. Chem. Phys.
, vol.10
, Issue.4
, pp. 471-481
-
-
Chen, J.1
Brooks, C.L.2
-
50
-
-
73349107159
-
The AGBNP2 Implicit Solvation Model
-
Gallicchio, E.; Paris, K.; Levy, R. M. The AGBNP2 Implicit Solvation Model J. Chem. Theory Comput. 2009, 5 (9) 2544-2564 10.1021/ct900234u
-
(2009)
J. Chem. Theory Comput.
, vol.5
, Issue.9
, pp. 2544-2564
-
-
Gallicchio, E.1
Paris, K.2
Levy, R.M.3
-
51
-
-
0042208326
-
On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent Interaction Energy
-
Levy, R. M.; Zhang, L. Y.; Gallicchio, E.; Felts, A. K. On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent Interaction Energy J. Am. Chem. Soc. 2003, 125 (31) 9523-9530 10.1021/ja029833a
-
(2003)
J. Am. Chem. Soc.
, vol.125
, Issue.31
, pp. 9523-9530
-
-
Levy, R.M.1
Zhang, L.Y.2
Gallicchio, E.3
Felts, A.K.4
-
52
-
-
33744822783
-
Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
-
Wagoner, J. A.; Baker, N. A. Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms Proc. Natl. Acad. Sci. U. S. A. 2006, 103 (22) 8331-8336 10.1073/pnas.0600118103
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, Issue.22
, pp. 8331-8336
-
-
Wagoner, J.A.1
Baker, N.A.2
-
53
-
-
4444323489
-
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
-
Wagoner, J.; Baker, N. A. Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models J. Comput. Chem. 2004, 25 (13) 1623-1629 10.1002/jcc.20089
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.13
, pp. 1623-1629
-
-
Wagoner, J.1
Baker, N.A.2
-
54
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 1990, 112 (16) 6127-6129 10.1021/ja00172a038
-
(1990)
J. Am. Chem. Soc.
, vol.112
, Issue.16
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
55
-
-
36148936033
-
Analysis of integral expressions for effective Born radii
-
Mongan, J.; Svrcek-Seiler, W. A.; Onufriev, A. Analysis of integral expressions for effective Born radii J. Chem. Phys. 2007, 127 (18) 185101 10.1063/1.2783847
-
(2007)
J. Chem. Phys.
, vol.127
, Issue.18
, pp. 185101
-
-
Mongan, J.1
Svrcek-Seiler, W.A.2
Onufriev, A.3
-
56
-
-
0141453063
-
Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
-
Grycuk, T. Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation J. Chem. Phys. 2003, 119 (9) 4817-4826 10.1063/1.1595641
-
(2003)
J. Chem. Phys.
, vol.119
, Issue.9
, pp. 4817-4826
-
-
Grycuk, T.1
-
57
-
-
78651330129
-
Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii
-
Aguilar, B.; Shadrach, R.; Onufriev, A. V. Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii J. Chem. Theory Comput. 2010, 6 (12) 3613-3630 10.1021/ct100392h
-
(2010)
J. Chem. Theory Comput.
, vol.6
, Issue.12
, pp. 3613-3630
-
-
Aguilar, B.1
Shadrach, R.2
Onufriev, A.V.3
-
58
-
-
0037110472
-
Effective Born radii in the generalized Born approximation: The importance of being perfect
-
Onufriev, A.; Case, D. A.; Bashford, D. Effective Born radii in the generalized Born approximation: The importance of being perfect J. Comput. Chem. 2002, 23 (14) 1297-1304 10.1002/jcc.10126
-
(2002)
J. Comput. Chem.
, vol.23
, Issue.14
, pp. 1297-1304
-
-
Onufriev, A.1
Case, D.A.2
Bashford, D.3
-
59
-
-
14544285906
-
Comparative Study of Generalized Born Models:Born Radii and Peptide Folding
-
Zhu, J.; Alexov, E.; Honig, B. Comparative Study of Generalized Born Models:Born Radii and Peptide Folding J. Phys. Chem. B 2005, 109 (7) 3008-3022 10.1021/jp046307s
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.7
, pp. 3008-3022
-
-
Zhu, J.1
Alexov, E.2
Honig, B.3
-
60
-
-
33846538819
-
The NEWUOA software for unconstrained optimization without derivatives
-
Pillo, G. Roma, M. Springer
-
Powell, M. J. D. The NEWUOA software for unconstrained optimization without derivatives. In Large-Scale Nonlinear Optimization; Pillo, G.; Roma, M., Eds.; Springer: 2006; Vol. 83, pp 255-297.
-
(2006)
Large-Scale Nonlinear Optimization
, vol.83
, pp. 255-297
-
-
Powell, M.J.D.1
-
61
-
-
84879693300
-
Derivative-free optimization: a review of algorithms and comparison of software implementations
-
Rios, L.; Sahinidis, N. Derivative-free optimization: a review of algorithms and comparison of software implementations J Glob Optim 2013, 56 (3) 1247-1293 10.1007/s10898-012-9951-y
-
(2013)
J Glob Optim
, vol.56
, Issue.3
, pp. 1247-1293
-
-
Rios, L.1
Sahinidis, N.2
-
62
-
-
0041711007
-
UOBYQA: unconstrained optimization by quadratic approximation
-
Powell, M. J. D. UOBYQA: unconstrained optimization by quadratic approximation Math. Program. 2002, 92 (3) 555-582 10.1007/s101070100290
-
(2002)
Math. Program.
, vol.92
, Issue.3
, pp. 555-582
-
-
Powell, M.J.D.1
-
63
-
-
0030953141
-
Molecular Dynamics Simulations Highlight the Structural Differences among DNA:DNA, RNA:RNA, and DNA:RNA Hybrid Duplexes
-
Cheatham, T. E.; Kollman, P. A. Molecular Dynamics Simulations Highlight the Structural Differences among DNA:DNA, RNA:RNA, and DNA:RNA Hybrid Duplexes J. Am. Chem. Soc. 1997, 119 (21) 4805-4825 10.1021/ja963641w
-
(1997)
J. Am. Chem. Soc.
, vol.119
, Issue.21
, pp. 4805-4825
-
-
Cheatham, T.E.1
Kollman, P.A.2
-
64
-
-
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 (2) 926-935 10.1063/1.445869
-
(1983)
J. Chem. Phys.
, vol.79
, Issue.2
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
65
-
-
0019331504
-
Crystal structure analysis of a complete turn of B-DNA
-
Wing, R.; Drew, H.; Takano, T.; Broka, C.; Tanaka, S.; Itakura, K.; Dickerson, R. Crystal structure analysis of a complete turn of B-DNA Nature 1980, 287 (5784) 755 10.1038/287755a0
-
(1980)
Nature
, vol.287
, Issue.5784
, pp. 755
-
-
Wing, R.1
Drew, H.2
Takano, T.3
Broka, C.4
Tanaka, S.5
Itakura, K.6
Dickerson, R.7
-
66
-
-
0032530719
-
A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA
-
Allen, M. D.; Yamasaki, K.; Ohme Takagi, M.; Tateno, M.; Suzuki, M. A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA EMBO J. 1998, 17 (18) 5484-5496 10.1093/emboj/17.18.5484
-
(1998)
EMBO J.
, vol.17
, Issue.18
, pp. 5484-5496
-
-
Allen, M.D.1
Yamasaki, K.2
Ohme Takagi, M.3
Tateno, M.4
Suzuki, M.5
-
67
-
-
42449095007
-
Towards a molecular dynamics consensus view of B-DNA flexibility
-
Pérez, A.; Lankas, F.; Luque, F. J.; Orozco, M. Towards a molecular dynamics consensus view of B-DNA flexibility Nucleic Acids Res. 2008, 36 (7) 2379-2394 10.1093/nar/gkn082
-
(2008)
Nucleic Acids Res.
, vol.36
, Issue.7
, pp. 2379-2394
-
-
Pérez, A.1
Lankas, F.2
Luque, F.J.3
Orozco, M.4
-
68
-
-
0028800948
-
Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA
-
Zhu, L.; Chou, S.-H.; Xu, J.; Reid, B. R. Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA Nat. Struct. Biol. 1995, 2 (11) 1012-1017 10.1038/nsb1195-1012
-
(1995)
Nat. Struct. Biol.
, vol.2
, Issue.11
, pp. 1012-1017
-
-
Zhu, L.1
Chou, S.-H.2
Xu, J.3
Reid, B.R.4
-
69
-
-
80455168345
-
Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations
-
Kannan, S.; Zacharias, M. Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations Nucleic Acids Res. 2011, 39 (19) 8271-8280 10.1093/nar/gkr541
-
(2011)
Nucleic Acids Res.
, vol.39
, Issue.19
, pp. 8271-8280
-
-
Kannan, S.1
Zacharias, M.2
-
70
-
-
77449092763
-
High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA
-
Nozinovic, S.; Fürtig, B.; Jonker, H. R. A.; Richter, C.; Schwalbe, H. High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA Nucleic Acids Res. 2010, 38 (2) 683-694 10.1093/nar/gkp956
-
(2010)
Nucleic Acids Res.
, vol.38
, Issue.2
, pp. 683-694
-
-
Nozinovic, S.1
Fürtig, B.2
Jonker, H.R.A.3
Richter, C.4
Schwalbe, H.5
-
71
-
-
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 (4) 2516-2524 10.1529/biophysj.104.055087
-
(2005)
Biophys. J.
, vol.88
, Issue.4
, pp. 2516-2524
-
-
Sorin, E.J.1
Rhee, Y.M.2
Pande, V.S.3
-
72
-
-
84875989318
-
Computer Folding of RNA Tetraloops? Are We There Yet?
-
Kührová, P.; Banáš, P.; Best, R. B.; Šponer, J.; Otyepka, M. Computer Folding of RNA Tetraloops? Are We There Yet? J. Chem. Theory Comput. 2013, 9 (4) 2115-2125 10.1021/ct301086z
-
(2013)
J. Chem. Theory Comput.
, vol.9
, Issue.4
, pp. 2115-2125
-
-
Kührová, P.1
Banáš, P.2
Best, R.B.3
Šponer, J.4
Otyepka, M.5
-
73
-
-
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. i.; Mládek, A. t.; Banáš, P.; Cheatham, T. E., III; 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 (9) 2886-2902 10.1021/ct200162x
-
(2011)
J. Chem. Theory Comput.
, vol.7
, Issue.9
, pp. 2886-2902
-
-
Zgarbová, M.1
Otyepka, M.2
Šponer, J.I.3
Mládek, A.T.4
Banáš, P.5
Cheatham, T.E.6
Jurecka, P.7
-
74
-
-
22944441922
-
Incorporating variable dielectric environments into the generalized Born model
-
Sigalov, G.; Scheffel, P.; Onufriev, A. Incorporating variable dielectric environments into the generalized Born model J. Chem. Phys. 2005, 122 (9) 094511-15 10.1063/1.1857811
-
(2005)
J. Chem. Phys.
, vol.122
, Issue.9
, pp. 094511-094515
-
-
Sigalov, G.1
Scheffel, P.2
Onufriev, A.3
-
75
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins: Struct., Funct., Genet. 2006, 65 (3) 712-725 10.1002/prot.21123
-
(2006)
Proteins: Struct., Funct., Genet.
, vol.65
, Issue.3
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
76
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
-
Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23 (3) 327-341 10.1016/0021-9991(77)90098-5
-
(1977)
J. Comput. Phys.
, vol.23
, Issue.3
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.3
-
77
-
-
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 (8) 3684-3690 10.1063/1.448118
-
(1984)
J. Chem. Phys.
, vol.81
, Issue.8
, 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
-
78
-
-
0033468737
-
Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects
-
Srinivasan, J.; Trevathan, M. W.; Beroza, P.; Case, D. A. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects Theor. Chem. Acc. 1999, 101 (6) 426-434 10.1007/s002140050460
-
(1999)
Theor. Chem. Acc.
, vol.101
, Issue.6
, pp. 426-434
-
-
Srinivasan, J.1
Trevathan, M.W.2
Beroza, P.3
Case, D.A.4
-
79
-
-
84880022273
-
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
-
Roe, D. R.; Cheatham, T. E. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data J. Chem. Theory Comput. 2013, 9 (7) 3084-3095 10.1021/ct400341p
-
(2013)
J. Chem. Theory Comput.
, vol.9
, Issue.7
, pp. 3084-3095
-
-
Roe, D.R.1
Cheatham, T.E.2
-
80
-
-
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 (17) 5917-5929 10.1093/nar/gkp608
-
(2009)
Nucleic Acids Res.
, vol.37
, Issue.17
, pp. 5917-5929
-
-
Lavery, R.1
Moakher, M.2
Maddocks, J.H.3
Petkeviciute, D.4
Zakrzewska, K.5
-
81
-
-
0037423728
-
Structure of a G-quadruplex-Ligand Complex
-
Haider, S. M.; Parkinson, G. N.; Neidle, S. Structure of a G-quadruplex-Ligand Complex J. Mol. Biol. 2003, 326 (1) 117-125 10.1016/S0022-2836(02)01354-2
-
(2003)
J. Mol. Biol.
, vol.326
, Issue.1
, pp. 117-125
-
-
Haider, S.M.1
Parkinson, G.N.2
Neidle, S.3
-
82
-
-
0029120978
-
Terminal Base-Pairs of Oligodeoxynucleotides - Imino Proton-Exchange and Fraying
-
Nonin, S.; Leroy, J. L.; Gueron, M. Terminal Base-Pairs of Oligodeoxynucleotides-Imino Proton-Exchange and Fraying Biochemistry 1995, 34 (33) 10652-10659 10.1021/bi00033a041
-
(1995)
Biochemistry
, vol.34
, Issue.33
, pp. 10652-10659
-
-
Nonin, S.1
Leroy, J.L.2
Gueron, M.3
-
83
-
-
79751535311
-
Improving the description of salt bridge strength and geometry in a Generalized Born model
-
Shang, Y.; Nguyen, H.; Wickstrom, L.; Okur, A.; Simmerling, C. Improving the description of salt bridge strength and geometry in a Generalized Born model J. Mol. Graphics Modell. 2011, 29 (5) 676-684 10.1016/j.jmgm.2010.11.013
-
(2011)
J. Mol. Graphics Modell.
, vol.29
, Issue.5
, pp. 676-684
-
-
Shang, Y.1
Nguyen, H.2
Wickstrom, L.3
Okur, A.4
Simmerling, C.5
-
84
-
-
84881521091
-
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
-
Stadlbauer, P.; Krepl, M.; Cheatham, T. E.; Koča, J.; Šponer, J. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations Nucleic Acids Res. 2013, 41 (14) 7128-7143 10.1093/nar/gkt412
-
(2013)
Nucleic Acids Res.
, vol.41
, Issue.14
, pp. 7128-7143
-
-
Stadlbauer, P.1
Krepl, M.2
Cheatham, T.E.3
Koča, J.4
Šponer, J.5
-
85
-
-
33645401742
-
G-Quadruplexes Can Maintain Their Structure in the Gas Phase
-
Rueda, M.; Luque, F. J.; Orozco, M. G-Quadruplexes Can Maintain Their Structure in the Gas Phase J. Am. Chem. Soc. 2006, 128 (11) 3608-3619 10.1021/ja055936s
-
(2006)
J. Am. Chem. Soc.
, vol.128
, Issue.11
, pp. 3608-3619
-
-
Rueda, M.1
Luque, F.J.2
Orozco, M.3
-
86
-
-
0029941154
-
Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution
-
Cheatham, T. E., III; Kollman, P. A. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution J. Mol. Biol. 1996, 259 (3) 434-444 10.1006/jmbi.1996.0330
-
(1996)
J. Mol. Biol.
, vol.259
, Issue.3
, pp. 434-444
-
-
Cheatham, T.E.1
Kollman, P.A.2
-
87
-
-
0033064123
-
Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model
-
Williams, D. J.; Hall, K. B. Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model Biophys. J. 1999, 76 (6) 3192-3205 10.1016/S0006-3495(99)77471-0
-
(1999)
Biophys. J.
, vol.76
, Issue.6
, pp. 3192-3205
-
-
Williams, D.J.1
Hall, K.B.2
-
88
-
-
20644449471
-
Modification of the Generalized Born Model Suitable for Macromolecules
-
Onufriev, A.; Bashford, D.; Case, D. A. Modification of the Generalized Born Model Suitable for Macromolecules J. Phys. Chem. B 2000, 104 (15) 3712-3720 10.1021/jp994072s
-
(2000)
J. Phys. Chem. B
, vol.104
, Issue.15
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
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