-
4
-
-
0028832014
-
Fluorescent d(CGCGAATT CGCG): Characterization of major groove polarity and study of minor groove interactions through a major groove semantophore conjugate
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 159-164
-
-
Barawkar, D.A.1
Ganesh, K.N.2
-
6
-
-
0026742978
-
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
-
(1992)
Biophys. J.
, vol.63
, pp. 751-759
-
-
Berman, H.M.1
Olson, W.K.2
Beveridge, D.L.3
Westbrook, J.4
Gelbin, A.5
Demeny, T.6
Hsieh, S.H.7
Srinivasan, A.R.8
Schneider, B.9
-
7
-
-
0033954256
-
The Protein Data Bank
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
11
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
(1983)
J. Comp. Chem.
, vol.4
, 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
-
13
-
-
0004268506
-
-
University of California, San Francisco
-
(1999)
AMBER 6
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham T.E. III4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Tsui, V.13
Radmer, R.J.14
Duan, Y.15
Pitera, J.16
Massova, I.17
Seibel, G.L.18
Singh, U.C.19
Weiner, P.K.20
Kollman, P.A.21
more..
-
15
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
(1995)
J. Am. Chem. Soc.
, vol.117
, 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
-
16
-
-
3342936878
-
An SCF solvation model for the hydrophobic effect and absolute free-energies of aqueous solvation
-
(1992)
Science
, vol.256
, pp. 213-217
-
-
Cramer, C.J.1
Truhlar, D.G.2
-
22
-
-
0000742485
-
X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution
-
(1998)
Biopolymers
, vol.48
, pp. 234-252
-
-
Egli, M.1
Tereshko, V.2
Teplova, M.3
Minasov, G.4
Joachimiak, A.5
Sanishvili, R.6
Weeks, C.M.7
Miller, R.8
Maier, M.A.9
An, H.10
Dan Cook, P.11
Manoharan, M.12
-
24
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
(2000)
J. Comp. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerell A.D., Jr.2
-
27
-
-
0031041812
-
NMR solution structures of stereoisometric covalent polycyclic aromatic carcinogen-DNA adduct: Principles, patterns, and diversity
-
(1997)
Chem. Res. Toxicol.
, vol.10
, pp. 111-146
-
-
Geacintov, N.E.1
Cosman, M.2
Hingerty, B.E.3
Amin, S.4
Broyde, S.5
Patel, D.J.6
-
29
-
-
0000755144
-
Effects of dielectric saturation upon the diffuse double layer and the free energy of hydration of ions
-
(1950)
J. Chem. Phys.
, vol.18
, pp. 903-909
-
-
Grahame, D.C.1
-
35
-
-
0011930746
-
Theory of hydrophobic bonding. 2. Correlation of hydrocarbon solubility in water with solvent cavity surface-area
-
(1972)
J. Phys. Chem.
, vol.76
, pp. 2754-2759
-
-
Hermann, R.B.1
-
42
-
-
0031556948
-
DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide X-ray crystal structures
-
(1997)
J. Mol. Biol.
, vol.265
, pp. 603-619
-
-
Hunter, C.A.1
Lu, X.J.2
-
50
-
-
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
-
57
-
-
0017895903
-
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
-
(1978)
Quart. Revs. Biophys.
, vol.11
, pp. 179-246
-
-
Manning, G.S.1
-
64
-
-
0033012333
-
A self-consistent, microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins
-
(1999)
Biophys. J.
, vol.77
, pp. 3-22
-
-
Mehler, E.L.1
Guarnieri, F.2
-
66
-
-
84985735758
-
Spatial configurations of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides
-
(1972)
Biopolymers
, vol.11
, pp. 25-56
-
-
Olson, W.K.1
Flory, P.J.2
-
67
-
-
0017817559
-
Spatial configuration of ordered polynucleotide chains. V. Conformatonal energy estimates of helical structure
-
(1978)
Biopolymers
, vol.17
, pp. 1015-1040
-
-
Olson, W.K.1
-
68
-
-
0019923858
-
How flexible is the furanose ring? 2. An updated potential energy estimate
-
(1982)
J. Am. Chem. Soc.
, vol.104
, pp. 278-286
-
-
Olson, W.K.1
-
74
-
-
0001008029
-
Efficient method for finding minimum of function of several variables without calculating derivatives
-
(1964)
Comput. J.
, vol.7
, pp. 155-159
-
-
Powell, M.J.D.1
-
77
-
-
0027315056
-
Synthesis of oligodeoxynucleotides containing the C-nucleoside and 2′-deoxy-2′-fluoro-ara-nucleoside moieties by the H-phosphonate method
-
(1993)
Nucleosides Nucleotides
, vol.12
, pp. 381-401
-
-
Rosenberg, I.1
Soler, J.F.2
Tocik, Z.3
Ren, W.Y.4
Ciszewski, L.A.5
Kois, P.6
Pankiewicz, K.W.7
Spassova, M.8
Watanabe, K.A.9
-
78
-
-
0001528269
-
The dielectric constant of electrolytes
-
(1926)
Phys. Z.
, vol.27
, pp. 206-208
-
-
Sack, V.H.1
-
79
-
-
0000677203
-
The dielectric constants of solutions of electrolytes at small concentrations
-
(1927)
Phys. Z.
, vol.28
, pp. 199-210
-
-
Sack, V.H.1
-
86
-
-
0031552364
-
X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 595-623
-
-
Shatsky-Schwartz, M.1
Arbuckle, N.D.2
Eisenstein, M.3
Rabinovich, D.4
Bareket-Samish, A.5
Haran, T.E.6
Luisi, B.F.7
Shakked, Z.8
-
90
-
-
0026002638
-
Structures of the (+)- and (-)-trans-7,8-dihydroxy-anti-9,10-epoxy- 7,8,9,10-tetrahydrobenzo(a)pyrene adducts to guanine-N2 in a duplex dodecamer
-
(1991)
Cancer Res.
, vol.51
, pp. 3482-3492
-
-
Singh, S.B.1
Hingerty, B.E.2
Singh, U.C.3
Greenberg, J.P.4
Geacintov, N.E.5
Broyde, S.6
-
91
-
-
0027370181
-
Theoretical analysis of the base stacking in DNA: Choice of the force field and a comparison with the oligonucleotide crystal structures
-
(1993)
J. Biomol. Struct. Dyn.
, vol.11
, pp. 277-292
-
-
Sponer, J.1
Kypr, J.2
-
101
-
-
14244273182
-
Theory and applications of the generalized Born solvation model in macromolecular simulations
-
(2001)
Biopolymers
, vol.56
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
102
-
-
0023459640
-
Re-refinement of the B-dodecamer d(CGCGAATTCGCG) with a comparative analysis of the solvent in it and in the Z-hexamer d(5BrCG5BrCG5BrCG)
-
(1987)
J. Biomol. Struct. Dyn.
, vol.5
, pp. 581-600
-
-
Westhof, E.1
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