-
1
-
-
0022432240
-
Structural junctions in DNA: The influence of flanking sequence on nuclease digestion specificities
-
H.R. Drew, A.A. Travers. Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities. Nucleic Acids Res., 13, 4445 (1985).
-
(1985)
Nucleic Acids Res
, vol.13
, pp. 4445
-
-
Drew, H.R.1
Travers, A.A.2
-
2
-
-
0019843568
-
Structure of a B-DNA dodecamer III. Geometry of hydration
-
H.R. Drew, R.E. Dickerson. Structure of a B-DNA dodecamer III. Geometry of hydration. J. Mol. Biol., 151, 535 (1981).
-
(1981)
J. Mol. Biol
, vol.151
, pp. 535
-
-
Drew, H.R.1
Dickerson, R.E.2
-
3
-
-
0035812654
-
Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: A comparative analysis of T-A and A-T steps within A-tracts
-
D.R. Mack, T.K. Chiu, R.E. Dickerson. Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts. J. Mol. Blol., 312, 1037 (2001).
-
(2001)
J. Mol. Blol
, vol.312
, pp. 1037
-
-
Mack, D.R.1
Chiu, T.K.2
Dickerson, R.E.3
-
4
-
-
10044257912
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps
-
D.L. Beveridge, et al. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys. J., 87, 3799 (2004).
-
(2004)
Biophys. J
, vol.87
, pp. 3799
-
-
Beveridge, D.L.1
-
5
-
-
28044444099
-
Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: Toward understanding the indirect readout mechanism in protein-DNA recognition
-
M.J. Arauzo-Bravo, S. Fujii, H. Kono, S. Ahmad, A. Sarai. Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition. J. Am. Chem. Soc., 127, 16074 (2005).
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 16074
-
-
Arauzo-Bravo, M.J.1
Fujii, S.2
Kono, H.3
Ahmad, S.4
Sarai, A.5
-
6
-
-
0013059667
-
-
University of California, San Francisco
-
D.A. Case, et al. AMBER7, University of California, San Francisco (2002).
-
(2002)
AMBER7
-
-
Case, D.A.1
-
7
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
J.M. Wang, P. Cieplak, P.A. Kollman. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049 (2000).
-
(2000)
J. Comput. Chem
, vol.21
, pp. 1049
-
-
Wang, J.M.1
Cieplak, P.2
Kollman, P.A.3
-
8
-
-
0032922174
-
A modified version of the Cornell el al. force field with improved suger pucker phases and helical repeat
-
T.E. Cheatham III, P. Cieplak, P.A. Kollman. A modified version of the Cornell el al. force field with improved suger pucker phases and helical repeat. J. Biomol. Struct. Dyn., 16, 845 (1999).
-
(1999)
J. Biomol. Struct. Dyn
, vol.16
, pp. 845
-
-
Cheatham III, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
9
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926 (1983).
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
10
-
-
33846823909
-
Particle mesh Ewald: An N - log(N) method for Ewald sums in large systems
-
T. Darden, D. York, L. Pedersen. Particle mesh Ewald: an N - log(N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089 (1993).
-
(1993)
J. Chem. Phys
, vol.98
, pp. 10089
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
11
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, J.R. Haak, Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684 (1984).
-
(1984)
J. Chem. Phys
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
12
-
-
0037102493
-
Effect of a neutralized phosphate backbone on the minor groove of B-DNA: Molecular dynamics simulation studies
-
D. Hamelberg, L.D. Williams, W.D. Wilson. Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies. Nucleic Acids Res., 30, 3615 (2002).
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3615
-
-
Hamelberg, D.1
Williams, L.D.2
Wilson, W.D.3
-
13
-
-
0034714010
-
1Å crystal structures of B-DNA reveal sequence specific binding and groove-specific bending of DNA by magnesium and calcium
-
T.K. Chiu, R.E. Dickerson. 1Å crystal structures of B-DNA reveal sequence specific binding and groove-specific bending of DNA by magnesium and calcium. J. Mol. Biol., 301, 915 (2000).
-
(2000)
J. Mol. Biol
, vol.301
, pp. 915
-
-
Chiu, T.K.1
Dickerson, R.E.2
-
14
-
-
0032544507
-
Two distinct modes of protein-induced bending in DNA
-
M.A. El Hassan, C.R. Calladine. Two distinct modes of protein-induced bending in DNA. J. Mol. Biol., 282, 331 (1998).
-
(1998)
J. Mol. Biol
, vol.282
, pp. 331
-
-
El Hassan, M.A.1
Calladine, C.R.2
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