-
2
-
-
0019387686
-
Structure of a B-DNA dodecamer: Influence of base sequence on helix structure
-
Dickerson,R.E. and Drew,H.R. (1981) Structure of a B-DNA dodecamer: influence of base sequence on helix structure. J. Mol. Biol., 149, 761-786.
-
(1981)
J. Mol. Biol.
, vol.149
, pp. 761-786
-
-
Dickerson, R.E.1
Drew, H.R.2
-
3
-
-
0023513912
-
The structure of an oligo(dA)·oligo(dT) tract and its biological implications
-
Nelson,H.C., Finch,J.T., Luisi,B.F. and Klug,A. (1987) The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature, 330, 221-226.
-
(1987)
Nature
, vol.330
, pp. 221-226
-
-
Nelson, H.C.1
Finch, J.T.2
Luisi, B.F.3
Klug, A.4
-
4
-
-
0019843568
-
Structure of a B-DNA dodecamer. III. Geometry of hydration
-
Drew,H.R. and Dickerson,R.E. (1981) Structure of a B-DNA dodecamer. III. Geometry of hydration. J. Mol. Biol., 151, 535-556.
-
(1981)
J. Mol. Biol.
, vol.151
, pp. 535-556
-
-
Drew, H.R.1
Dickerson, R.E.2
-
5
-
-
0020692923
-
Ordered water structure around a B-DNA dodecamer. A quantitative study
-
Kopka,M.L., Fratini,A.V., Drew,H.R. and Dickerson,R.E. (1983) Ordered water structure around a B-DNA dodecamer. A quantitative study. J. Mol. Biol., 163, 129-146.
-
(1983)
J. Mol. Biol.
, vol.163
, pp. 129-146
-
-
Kopka, M.L.1
Fratini, A.V.2
Drew, H.R.3
Dickerson, R.E.4
-
6
-
-
0032387836
-
Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
-
Shui,X., Sines,C.C., McFail-Isom,L., VanDerveer,D. and Williams,L.D. (1998) Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry, 37, 16877-16887.
-
(1998)
Biochemistry
, vol.37
, pp. 16877-16887
-
-
Shui, X.1
Sines, C.C.2
McFail-Isom, L.3
VanDerveer, D.4
Williams, L.D.5
-
7
-
-
0032499635
-
The B-DNA dodecamer at high resolution reveals a spine of water on sodium
-
Shui,X., McFail-Isom,L., Hu,G.G. and Williams,L.D. (1998) The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry, 37, 8341-8355.
-
(1998)
Biochemistry
, vol.37
, pp. 8341-8355
-
-
Shui, X.1
McFail-Isom, L.2
Hu, G.G.3
Williams, L.D.4
-
8
-
-
0033585580
-
The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution
-
Tereshko,V., Minasov,G. and Egli,M. (1999) The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J. Am. Chem. Soc., 121, 470-471.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 470-471
-
-
Tereshko, V.1
Minasov, G.2
Egli, M.3
-
9
-
-
0033600794
-
Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG
-
Chiu,T.K., Kaczor-Grzeskowiak,M. and Dickerson,R.E. (1999) Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG. J. Mol. Biol., 292, 589-608.
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 589-608
-
-
Chiu, T.K.1
Kaczor-Grzeskowiak, M.2
Dickerson, R.E.3
-
10
-
-
0033594498
-
A 'hydrat-ion' spine in a B-DNA minor groove
-
Tereshko,V., Minasov,G. and Egli,M. (1999) A 'hydrat-ion' spine in a B-DNA minor groove. J. Am. Chem. Soc., 121, 3590-3595.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 3590-3595
-
-
Tereshko, V.1
Minasov, G.2
Egli, M.3
-
11
-
-
0033150892
-
DNA structure: Cations in charge?
-
McFail-Isom,L., Sines,C.C. and Williams,L.D. (1999) DNA structure: cations in charge? Curr. Opin. Struct. Biol., 9, 298-304.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 298-304
-
-
McFail-Isom, L.1
Sines, C.C.2
Williams, L.D.3
-
12
-
-
0035964383
-
Locating monovalent cations in the grooves of B-DNA
-
Howerton,S.B., Sines,C.C., VanDerveer,D. and Williams,L.D. (2001) Locating monovalent cations in the grooves of B-DNA. Biochemistry. 40, 10023-10031.
-
(2001)
Biochemistry
, vol.40
, pp. 10023-10031
-
-
Howerton, S.B.1
Sines, C.C.2
VanDerveer, D.3
Williams, L.D.4
-
13
-
-
0033605083
-
Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
-
Hud,N.V., Sklenar,V. and Feigon,J. (1999) Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J. Mol. Biol., 286, 651-660.
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 651-660
-
-
Hud, N.V.1
Sklenar, V.2
Feigon, J.3
-
14
-
-
0034681195
-
Sequence-specific binding of counterions to B-DNA
-
Denisov,V.P. and Halle,B. (2000) Sequence-specific binding of counterions to B-DNA. Proc. Natl Acad. Sci. USA, 97, 629-633.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 629-633
-
-
Denisov, V.P.1
Halle, B.2
-
15
-
-
14244271476
-
Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
-
Cheatham,T.E.,III and Young,M.A. (2001) Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers, 56, 232-256.
-
(2001)
Biopolymers
, vol.56
, pp. 232-256
-
-
Cheatham III, T.E.1
Young, M.A.2
-
16
-
-
0031047279
-
Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
-
Young,M.A., Jarayam,B. and Beveridge,D.L. (1997) Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets. J. Am. Chem. Soc., 119, 59-69.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 59-69
-
-
Young, M.A.1
Jarayam, B.2
Beveridge, D.L.3
-
17
-
-
0034671291
-
DNA structure: What's in charge?
-
McConnell,K.J. and Beveridge,D.L. (2000) DNA structure: what's in charge? J. Mol. Biol., 304, 803-820.
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 803-820
-
-
McConnell, K.J.1
Beveridge, D.L.2
-
18
-
-
0034327565
-
Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
-
Hamelberg,D., McFail-Isom,L., Williams,L.D. and Wilson,W.D. (2000) Flexible structure of DNA: ion dependence of minor-groove structure and dynamics. J. Am. Chem. Soc., 122, 10513-10520.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 10513-10520
-
-
Hamelberg, D.1
McFail-Isom, L.2
Williams, L.D.3
Wilson, W.D.4
-
19
-
-
0037385644
-
Molecular dynamics simulations of A·T-rich oligomers: Sequence-specific binding of Na+ in the minor groove of B-DNA
-
Mocci,F. and Saba,G. (2003) Molecular dynamics simulations of A·T-rich oligomers: sequence-specific binding of Na+ in the minor groove of B-DNA. Biopolymers, 68, 471-485.
-
(2003)
Biopolymers
, vol.68
, pp. 471-485
-
-
Mocci, F.1
Saba, G.2
-
20
-
-
0032851951
-
Sodium and chlorine ions as part of the DNA solvation shell
-
Feig,M. and Pettitt,B.M. (1999) Sodium and chlorine ions as part of the DNA solvation shell. Biophys. J., 77, 1769-1781.
-
(1999)
Biophys. J.
, vol.77
, pp. 1769-1781
-
-
Feig, M.1
Pettitt, B.M.2
-
21
-
-
0036106375
-
On the competition between water, sodium ions, and spermine in binding to DNA: A molecular dynamics computer simulation study
-
Korolev,N., Lyubartsev,A.P., Laaksonen,A. and Nordenskiold,L. (2002) On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study. Biophys. J., 82, 2860-2875.
-
(2002)
Biophys. J.
, vol.82
, pp. 2860-2875
-
-
Korolev, N.1
Lyubartsev, A.P.2
Laaksonen, A.3
Nordenskiold, L.4
-
22
-
-
0034725528
-
Water and ion binding around RNA and DNA (C,G) oligomers
-
Auffinger,P. and Westhof,E. (2000) Water and ion binding around RNA and DNA (C,G) oligomers. J. Mol. Biol., 300, 1113-1131.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 1113-1131
-
-
Auffinger, P.1
Westhof, E.2
-
23
-
-
0035793219
-
Water and ion binding around r(UpA)12 and d(TpA)12 oligomers. Comparison with RNA and DNA (CpG)12 duplexes
-
Auffinger,P. and Westhof,E. (2001) Water and ion binding around r(UpA)12 and d(TpA)12 oligomers. Comparison with RNA and DNA (CpG)12 duplexes. J. Mol. Biol., 305, 1057-1072.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 1057-1072
-
-
Auffinger, P.1
Westhof, E.2
-
24
-
-
0037342509
-
DNA polymorphism: A comparison of force fields for nucleic acids
-
Reddy,S.Y., Leclerc,F. and Karplus,M. (2003) DNA polymorphism: a comparison of force fields for nucleic acids. Biophys. J., 84, 1421-1449.
-
(2003)
Biophys. J.
, vol.84
, pp. 1421-1449
-
-
Reddy, S.Y.1
Leclerc, F.2
Karplus, M.3
-
25
-
-
0037178070
-
Base flipping in DNA: Pathways and energetics studied with molecular dynamics simulations
-
Várnai,P. and Lavery,R. (2002) Base flipping in DNA: pathways and energetics studied with molecular dynamics simulations. J. Am. Chem. Soc., 124, 7272-7273.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 7272-7273
-
-
Várnai, P.1
Lavery, R.2
-
26
-
-
4544237789
-
-
AMBER 6. University of California, San Francisco, CA
-
Case,D.A., Pearlman,D.A., Caldwell,J.W., Cheatham,T.E.,III, Ross,W.S., Simmerling,C.L., Darden,T.A., Metz,K.M., Stanton,R.V., Cheng,A.L. et al. (1999) AMBER 6. University of California, San Francisco, CA.
-
(1999)
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Metz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
-
27
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang,J., Cieplak,P. and Kollman,P.A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049-1074.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
28
-
-
1842738520
-
Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties
-
Patra,M. and Karttunen,M. (2004) Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties. J. Comput. Chem., 25, 678-689.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 678-689
-
-
Patra, M.1
Karttunen, M.2
-
29
-
-
2942547665
-
Simulation and modeling of nucleic acid structure, dynamics and interactions
-
Cheatham,T.E.,III (2004) Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol., 14, 360-367.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 360-367
-
-
Cheatham III, T.E.1
-
30
-
-
1642525904
-
Influence of artificial periodicity and ionic strength in MD simulations of charged biomolecules employing lattice-sum methods
-
Kastenholtz,M.A. and Hünenberger,H.P. (2004) Influence of artificial periodicity and ionic strength in MD simulations of charged biomolecules employing lattice-sum methods. J. Phys. Chem. B, 108, 774-788.
-
(2004)
J. Phys. Chem. B.
, vol.108
, pp. 774-788
-
-
Kastenholtz, M.A.1
Hünenberger, H.P.2
-
31
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen,H.J.C., Postma,J.P.M., van Gunsteren,W.F., DiNola,A. and Haak,J.R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684-3690.
-
(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
-
32
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys., 23, 327-341.
-
(1977)
J. Comp. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
33
-
-
33846823909
-
Particle mesh ewald: An N-log(N) methods for Ewald sums in large systems
-
Darden,T., York,D. and Pedersen,L. (1993) Particle mesh ewald: an N-log(N) methods for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
34
-
-
0027304152
-
Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations
-
Brunne,R.M., Liepinsh,E., Otting,G., Wuthrich,K. and van Gunsteren.W.F. (1993) Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol., 231, 1040-1048.
-
(1993)
J. Mol. Biol.
, vol.231
, pp. 1040-1048
-
-
Brunne, R.M.1
Liepinsh, E.2
Otting, G.3
Wuthrich, K.4
van Gunsteren, W.F.5
-
35
-
-
0024539180
-
Defining the structure of irregular nucleic acids: Convention and principles
-
Lavery,R. and Sklenar,H. (1989) Defining the structure of irregular nucleic acids: convention and principles. J. Biomol. Struct. Dyn., 6, 655-667.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 655-667
-
-
Lavery, R.1
Sklenar, H.2
-
36
-
-
0028184697
-
Measuring the geometry of DNA grooves
-
Stofer,E. and Lavery,R. (1994) Measuring the geometry of DNA grooves. Biopolymers, 34, 337-346.
-
(1994)
Biopolymers
, vol.34
, pp. 337-346
-
-
Stofer, E.1
Lavery, R.2
-
37
-
-
0025283002
-
Electrostatic interactions in macromolecules: Theory and applications
-
Sharp,K.A. and Honig,B. (1990) Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Chem., 19, 301-332.
-
(1990)
Annu. Rev. Biophys. Chem.
, vol.19
, pp. 301-332
-
-
Sharp, K.A.1
Honig, B.2
-
38
-
-
0031807764
-
Diffusion of solvent around biomolecular solutes: A molecular dynamics simulation study
-
Makarov,V.A., Feig,M., Andrews,B.K. and Pettitt,B.M. (1998) Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. Biophys. J., 75, 150-158.
-
(1998)
Biophys. J.
, vol.75
, pp. 150-158
-
-
Makarov, V.A.1
Feig, M.2
Andrews, B.K.3
Pettitt, B.M.4
-
40
-
-
0001324374
-
Solvent structure, dynamics, and ion mobility in aqueous solutions at 25°C
-
Koneshan,S., Rasaiah,J.C., Lynden-Bell,R.M. and Lee,S.H. (1998) Solvent structure, dynamics, and ion mobility in aqueous solutions at 25°C. J. Phys. Chem. B, 102, 4193-4204.
-
(1998)
J. Phys. Chem. B.
, vol.102
, pp. 4193-4204
-
-
Koneshan, S.1
Rasaiah, J.C.2
Lynden-Bell, R.M.3
Lee, S.H.4
-
41
-
-
0000660497
-
The crystal and molecular structure of adenosine triphosphate
-
Kennard,O., Isaacs,N.W., Motherwell,W.D., Coppola,J.C., Wampler,D.L., Larson,A.C. and Watson,D.G. (1971) The crystal and molecular structure of adenosine triphosphate. Proc. R. Soc. Lond. A, 325, 401-436.
-
(1971)
Proc. R. Soc. Lond. A.
, vol.325
, pp. 401-436
-
-
Kennard, O.1
Isaacs, N.W.2
Motherwell, W.D.3
Coppola, J.C.4
Wampler, D.L.5
Larson, A.C.6
Watson, D.G.7
-
42
-
-
17944388579
-
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets
-
Reblova,K., Spackova,N., Sponer,J.E., Koca,J. and Sponer,J. (2003) Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res., 31, 6942-6952.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6942-6952
-
-
Reblova, K.1
Spackova, N.2
Sponer, J.E.3
Koca, J.4
Sponer, J.5
-
43
-
-
0037764044
-
Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E
-
Reblova,K., Spackova,N., Stefl,R., Csaszar,K., Koca,J., Leontis,N.B. and Sponer,J. (2003) Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophys. J., 84, 3564-3582.
-
(2003)
Biophys. J.
, vol.84
, pp. 3564-3582
-
-
Reblova, K.1
Spackova, N.2
Stefl, R.3
Csaszar, K.4
Koca, J.5
Leontis, N.B.6
Sponer, J.7
-
44
-
-
0042823487
-
Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates
-
Stefl,R., Cheatham,T.E.,III, Spackova,N., Fadrna,E., Berger,I., Koca,J. and Sponer,J. (2003) Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys. J., 85, 1787-1804.
-
(2003)
Biophys. J.
, vol.85
, pp. 1787-1804
-
-
Stefl, R.1
Cheatham III, T.E.2
Spackova, N.3
Fadrna, E.4
Berger, I.5
Koca, J.6
Sponer, J.7
-
45
-
-
0034836422
-
Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations
-
Spackova,N., Berger,I. and Sponer,J. (2001) Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. J. Am. Chem. Soc., 123, 3295-3307.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 3295-3307
-
-
Spackova, N.1
Berger, I.2
Sponer, J.3
-
46
-
-
0036569686
-
Bending of DNA by asymmetric charge neutralization: All-atom energy simulations
-
Kosikov,K.M., Gorin,A.A., Lu,X.-J., Olson,W.K. and Manning,G.S. (2002) Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. J. Am. Chem. Soc., 124, 4838-4847.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 4838-4847
-
-
Kosikov, K.M.1
Gorin, A.A.2
Lu, X.-J.3
Olson, W.K.4
Manning, G.S.5
-
47
-
-
0038713237
-
A unified model for the origin of DNA sequence-directed curvature
-
Hud,N.V. and Plavec,J. (2003) A unified model for the origin of DNA sequence-directed curvature. Biopolymers, 69, 144-159.
-
(2003)
Biopolymers
, vol.69
, pp. 144-159
-
-
Hud, N.V.1
Plavec, J.2
-
48
-
-
0025778738
-
Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA
-
Pearlman,D.A. and Kollman,P.A. (1991) Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA. J. Mol. Biol., 220, 457-479.
-
(1991)
J. Mol. Biol.
, vol.220
, pp. 457-479
-
-
Pearlman, D.A.1
Kollman, P.A.2
-
49
-
-
0027432486
-
Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data
-
Schmitz,U., Ulyanov,N.B., Kumar,A. and James,T.L. (1993) Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data. J. Mol. Biol., 234, 373-389.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 373-389
-
-
Schmitz, U.1
Ulyanov, N.B.2
Kumar, A.3
James, T.L.4
-
50
-
-
0009978483
-
DNA bending and sequence-dependent backbone conformation NMR and computer experiments
-
Ojha,R.P., Dhingra,M.M., Sarma,M.H., Shibata,M., Farrar,M., Turner,C.J. and Sarma,R.H. (1999) DNA bending and sequence-dependent backbone conformation NMR and computer experiments. Eur. J. Biochem., 265, 35-53.
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(1999)
Eur. J. Biochem.
, vol.265
, pp. 35-53
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Ojha, R.P.1
Dhingra, M.M.2
Sarma, M.H.3
Shibata, M.4
Farrar, M.5
Turner, C.J.6
Sarma, R.H.7
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