-
3
-
-
0001025102
-
Nucleic acid simulations
-
Becker, O., MacKerell, A. D., Jr., Roux, B., Watanabe, M., Eds.; Marcel Dekker: New York
-
(2001)
Computational Biochemistry and Biophysics
, pp. 441-463
-
-
MacKerell A.D., Jr.1
Nilsson, L.2
-
7
-
-
0032459726
-
Molecular dynamic simulations of environment and sequence dependent DNA conformations: The developments of the BMS nucleic acids force field and comparison with experimental results
-
(1998)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 487-509
-
-
Langley, D.R.1
-
9
-
-
0033801089
-
Localisation and dynamics of sodium counterions around DNA in solution from molecular dynamics simulation
-
(2000)
Eur. Biophys. J.
, vol.29
, pp. 57-60
-
-
Bonvin, A.M.J.J.1
-
10
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
Van Gunsteren, W.F.10
-
12
-
-
0345983594
-
Observations on the A versus B equilibrium in molecular dynamics simulations of duplex DNA and RNA
-
Ceontis, N. B.; SantaLucia, J., Jr., Eds.; ACS Symposium Series 682; American Chemical Society: Washington, DC
-
(1998)
Molecular Modeling of Nucleic Acids
, pp. 304-311
-
-
MacKerell A.D., Jr.1
-
21
-
-
0034314630
-
Theoretical methods for the description of the solvent effect in biomolecular systems
-
(2000)
Chem. Rev.
, vol.100
, pp. 4187-4225
-
-
Orozco, M.1
Luque, F.J.2
-
27
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham T.E. III15
-
29
-
-
0025600834
-
Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 9161-9175
-
-
Elber, R.1
Karplus, M.2
-
30
-
-
0034723010
-
Theoretical studies of the possible origin of intrinsic static bends in double helical DNA
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 12778-12785
-
-
Mazur, A.K.1
-
68
-
-
0033576252
-
Solution structure and dynamics of a complex between DNA and the antitumor bisnaphthalimide LU-79553: Intercalates ring flipping on the millisecond time scale
-
(1999)
Biochemistry
, vol.38
, pp. 15104-15115
-
-
Gallego, J.1
Reid, B.R.2
-
70
-
-
0032846562
-
Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation
-
(1999)
Biophys. J.
, vol.77
, pp. 1782-1800
-
-
Sen, S.1
Nilsson, L.2
-
71
-
-
0032881916
-
Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex
-
(1999)
Biophys. J.
, vol.77
, pp. 1801-1810
-
-
Sen, S.1
Nilsson, L.2
-
75
-
-
0031903790
-
Structural and dynamical effects of point mutations in the recognition helix of the glucocorticoid receptor DNA-binding domain
-
(1998)
Protein Eng.
, vol.11
, pp. 589-600
-
-
Eriksson, A.A.L.1
Nilsson, L.2
-
77
-
-
0033046722
-
Change in conformation by DNA-peptide association: Molecular dynamics of the hin-recombinase-hixl complex
-
(1999)
Biophys. J.
, vol.77
, pp. 123-138
-
-
Komeiji, Y.1
Uebayasi, M.2
-
90
-
-
0034669503
-
DNA-triplex stabilizing properties of 8-aminoguamine
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4531-4539
-
-
Soliva, R.1
Garcia, R.G.2
Bias, J.R.3
Eritja, R.4
Asensio, J.L.5
Gonzalez, C.6
Luque, F.J.7
Orozco, M.8
-
92
-
-
0033970274
-
Structural properties of hybrid triplex of polycation deoxyribonucleic S-methylthiourea (DNmt) strands with a complementary DNA strand, probed by nanosecond molecular dynamics
-
(2000)
J. Biomol. Struct. Dyn.
, vol.17
, pp. 629-643
-
-
Luo, J.1
Bruice, T.C.2
-
93
-
-
0033178533
-
Stabilization of DNA triple helices by a series of mono- and disubdtitued amidoanthraquinones
-
(1999)
Eur. J. Biochem.
, vol.263
, pp. 817-825
-
-
Keppler, M.D.1
Read, M.A.2
Perry, P.J.3
Trent, J.O.4
Jenkins, T.C.5
Reszka, A.P.6
Neidle, S.7
Fox, K.R.8
-
97
-
-
0033729881
-
Molecular dynamics of the anticodon domain of yeast tRNA(Phe): Codon-anticodon interaction
-
(2000)
Biophys. J.
, vol.79
, pp. 2276-2289
-
-
Lahiri, A.1
Nilsson, L.2
-
104
-
-
0032838372
-
Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution
-
(1999)
Biophys. J.
, vol.77
, pp. 1284-1305
-
-
Tang, Y.1
Nilsson, L.2
-
107
-
-
0034646574
-
Structure and thermodynamics of RNA-protein binding: Using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 1145-1158
-
-
Reyes, C.M.1
Kollman, P.A.2
-
108
-
-
0032513007
-
Aminoglycoside binding to the hammerhead ribozyme: A general model for the interaction of cationic antibiotics with RNA
-
(1998)
J. Mol. Biol.
, vol.276
, pp. 903-912
-
-
Hermann, T.1
Westhof, E.2
|