-
1
-
-
0026049574
-
Deuterium NMR investigation of backbone dynamics in the synthetic oligonucleotide [d(CGCGAATTCGCG)]2
-
Alam, T. M., J. Orban, and G. P. Drobny. 1991. Deuterium NMR investigation of backbone dynamics in the synthetic oligonucleotide [d(CGCGAATTCGCG)]2. Biochemistry. 30:9229-9237.
-
(1991)
Biochemistry
, vol.30
, pp. 9229-9237
-
-
Alam, T.M.1
Orban, J.2
Drobny, G.P.3
-
3
-
-
0000946971
-
Atomic coordinates and molecular conformations for DNA-DNA, RNA-RNA, and DNA-RNA helices
-
CRC Press, Boca Raton, FL
-
Arnott, S., P. J. Campbell-Smith, and R. Chandrasekaran. 1976. Atomic coordinates and molecular conformations for DNA-DNA, RNA-RNA, and DNA-RNA helices. In CRC Handbook of Biochemistry and Molecular Biology. CRC Press, Boca Raton, FL. 411-422.
-
(1976)
CRC Handbook of Biochemistry and Molecular Biology
, pp. 411-422
-
-
Arnott, S.1
Campbell-Smith, P.J.2
Chandrasekaran, R.3
-
4
-
-
0000828880
-
A simple test for evaluating the truncation effects in simulations of systems involving charged groups
-
Auffinger, P., and D. L. Beveridge. 1995. A simple test for evaluating the truncation effects in simulations of systems involving charged groups. Chem. Phys. Lett. 234:413.
-
(1995)
Chem. Phys. Lett.
, vol.234
, pp. 413
-
-
Auffinger, P.1
Beveridge, D.L.2
-
5
-
-
0024282309
-
Crystal and solution structures of the B-DNA dodecamer d(CGCAAATTTGCG) probed by Raman spectroscopy: Heterogeneity in the crystal does not persist in the solution structure
-
Benevides, J. M., A. H.-J. Wang, G. A. Va, J. H. V. B. Der Marel, and G. J. Thoma, Jr. 1988. Crystal and solution structures of the B-DNA dodecamer d(CGCAAATTTGCG) probed by Raman spectroscopy: heterogeneity in the crystal does not persist in the solution structure. Biochemistry. 27:931-938.
-
(1988)
Biochemistry
, vol.27
, pp. 931-938
-
-
Benevides, J.M.1
Wang, A.H.-J.2
Va, G.A.3
Der Marel, J.H.V.B.4
Thoma Jr., G.J.5
-
6
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, and A. DiNola. 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
-
7
-
-
0030417238
-
Nucleic acid crystallography: A view from the nucleic acids data base
-
Berman, H. M., A. Gelbin, and J. Westbrook. 1996. Nucleic acid crystallography: a view from the nucleic acids data base. Prog. Mol. Biol. Biophys. 66:255-298.
-
(1996)
Prog. Mol. Biol. Biophys.
, vol.66
, pp. 255-298
-
-
Berman, H.M.1
Gelbin, A.2
Westbrook, J.3
-
8
-
-
0026742978
-
The nucleic acid database: A comprehensive relational database of three-dimensional structures of nucleic acids
-
Berman, H. M., W. K. Olson, D. L. Beveridge, J. Westbrook, A. Gelbin, T. Demeny, S.-H. Hsieh, A. R. Srinivasan, and B. Schneider. 1992. The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:751-759.
-
(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
-
9
-
-
0000014013
-
Monte Carlo computer simulation studies of the equilibrium properties and structure of liquid water
-
American Chemical Society, Washington. DC
-
Beveridge, D. L., M. Mezei, P. K. Mehrotra, F. T. Marchese, G. Ravishanker, T. R. Vasu, and S. Swaminathan. 1983. Monte Carlo computer simulation studies of the equilibrium properties and structure of liquid water. In Molecular-Based Study of Fluids. American Chemical Society, Washington. DC. 297-351.
-
(1983)
Molecular-Based Study of Fluids
, pp. 297-351
-
-
Beveridge, D.L.1
Mezei, M.2
Mehrotra, P.K.3
Marchese, F.T.4
Ravishanker, G.5
Vasu, T.R.6
Swaminathan, S.7
-
11
-
-
0011156533
-
Molecular simulation studies on the d(CGCGAATTCGCG) duplex: Hydration, ion atmosphere, structure and dynamics
-
Adenine Press, New York
-
Beveridge, D. L., P. Subramanian, B. Jayaram, S. Swaminathan, and G. Ravishanker. 1990. Molecular simulation studies on the d(CGCGAATTCGCG) duplex: hydration, ion atmosphere, structure and dynamics. In Structure and Methods III. DNA AND RNA. Adenine Press, New York. 79-112.
-
(1990)
Structure and Methods III. DNA and RNA
, pp. 79-112
-
-
Beveridge, D.L.1
Subramanian, P.2
Jayaram, B.3
Swaminathan, S.4
Ravishanker, G.5
-
12
-
-
0002593973
-
Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers
-
Macmillan Press, London
-
Beveridge, D. L., S. Swaminathan, G. Ravishanker, J. M. Withka, J. Srinivasan, C. Prevost, S. Louise-May, D. R. Langley, F. M. DiCapua, and P. H. Bolton. 1993. Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers. In Water and Biological Molecules. Macmillan Press, London. 165-225.
-
(1993)
Water and Biological Molecules
, pp. 165-225
-
-
Beveridge, D.L.1
Swaminathan, S.2
Ravishanker, G.3
Withka, J.M.4
Srinivasan, J.5
Prevost, C.6
Louise-May, S.7
Langley, D.R.8
DiCapua, F.M.9
Bolton, P.H.10
-
13
-
-
0026253815
-
Condensation of DNA by multivalent cations: Considerations on mechanism
-
Bloomfield, V. A. 1991. Condensation of DNA by multivalent cations: considerations on mechanism. Biopolymers. 31:1471-1481.
-
(1991)
Biopolymers
, vol.31
, pp. 1471-1481
-
-
Bloomfield, V.A.1
-
14
-
-
0029941154
-
Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution
-
Cheatham, T. E., III, and P. A. Kollman. 1996. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol. 259:434-444.
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 434-444
-
-
Cheatham III, T.E.1
Kollman, P.A.2
-
15
-
-
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, J. L. Miller, T. Fox, T. A. Darden, and P. A. Kollman. 1995. 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. 117:4193-4194.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4193-4194
-
-
Cheatham III, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
16
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
-
(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 Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
17
-
-
0001972983
-
The DNA helix and how it is read
-
Dickerson, R. E. 1983. The DNA helix and how it is read. Sci. Am. 249:94-111.
-
(1983)
Sci. Am.
, vol.249
, pp. 94-111
-
-
Dickerson, R.E.1
-
18
-
-
0026702486
-
DNA structure from A to Z
-
Dickerson, R. E. 1991. DNA structure from A to Z. Methods Enzymol. 211:67-111.
-
(1991)
Methods Enzymol.
, vol.211
, pp. 67-111
-
-
Dickerson, R.E.1
-
19
-
-
0024454946
-
Definitions and nomenclature of nucleic acid structural parameters
-
Dickerson, R. E., M. Bansal, C. R. Calladine, S. Diekmann, W. N. Hunter, O. Kennard, E. von Kitzing, R. Lavery, H. C. M. Nelson, W. K. Olson, W. Saenger, Z. Shakked, H. Sklenar, D. M. Soumpasis, C. S. Tung, A. H. J. Wang, and V. B. Zhurkin. 1989. Definitions and nomenclature of nucleic acid structural parameters. EMBO J. 8:1-4.
-
(1989)
EMBO J.
, vol.8
, pp. 1-4
-
-
Dickerson, R.E.1
Bansal, M.2
Calladine, C.R.3
Diekmann, S.4
Hunter, W.N.5
Kennard, O.6
Von Kitzing, E.7
Lavery, R.8
Nelson, H.C.M.9
Olson, W.K.10
Saenger, W.11
Shakked, Z.12
Sklenar, H.13
Soumpasis, D.M.14
Tung, C.S.15
Wang, A.H.J.16
Zhurkin, V.B.17
-
20
-
-
0019387686
-
Structure of a B DNA dodecamer. II. Influence of base sequence on helix structure
-
Dickerson, R. E., and H. R. Drew. 1981. Structure of a B DNA dodecamer. II. 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
-
21
-
-
0023459625
-
The effect of crystal packing on oligonucleotide double helix structure
-
Dickerson, R. E., D. S. Goodsell, M. L. Kopka, and P. E. Pjura. 1987. The effect of crystal packing on oligonucleotide double helix structure. J. Biomol. Struct. Dyn. 5:557-579.
-
(1987)
J. Biomol. Struct. Dyn.
, vol.5
, pp. 557-579
-
-
Dickerson, R.E.1
Goodsell, D.S.2
Kopka, M.L.3
Pjura, P.E.4
-
22
-
-
0026323895
-
Polymophism, packing, resolution, and reliablity in single-crystal DNA oligomer analyses
-
Dickerson, R. E., K. Grzeskowiak, M. Grzeskowiak, M. L. Kopka, T. Larson, A. Lipanov, G. G. Prive, J. Quintana, P. Schultze, K. Yanagi, H. Yuan, and H.-C. Yoon. 1991. Polymophism, packing, resolution, and reliablity in single-crystal DNA oligomer analyses. Nucleosides Nucleotides. 10:3-24.
-
(1991)
Nucleosides Nucleotides
, vol.10
, pp. 3-24
-
-
Dickerson, R.E.1
Grzeskowiak, K.2
Grzeskowiak, M.3
Kopka, M.L.4
Larson, T.5
Lipanov, A.6
Prive, G.G.7
Quintana, J.8
Schultze, P.9
Yanagi, K.10
Yuan, H.11
Yoon, H.-C.12
-
23
-
-
0342565151
-
Base sequence, helix geometry, hydration and helix stability in B-DNA
-
Dickerson, R. E., M. L. Kopka, and P. Pjura. 1985. Base sequence, helix geometry, hydration and helix stability in B-DNA. Biol. Macromol. Assemblies. 2:37-126.
-
(1985)
Biol. Macromol. Assemblies.
, vol.2
, pp. 37-126
-
-
Dickerson, R.E.1
Kopka, M.L.2
Pjura, P.3
-
24
-
-
0008123541
-
Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract
-
DiGabriele, A. D., M. R. Sanderson, and T. A. Steitz. 1989. Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl. Acad. Sci. USA. 86:1816-1820.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 1816-1820
-
-
DiGabriele, A.D.1
Sanderson, M.R.2
Steitz, T.A.3
-
25
-
-
0019843568
-
Structure of a B-DNA dodecamer. III. Geometry of hydration
-
Drew, H. R., and R. E. Dickerson. 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
-
27
-
-
0019558179
-
Structure of a B DNA dodecamer. I. Conformation and dynamics
-
Drew, H. R., R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itikura, and R. E. Dickerson. 1981. Structure of a B DNA dodecamer. I. Conformation and dynamics. Proc. Natl. Acad. Sci. USA. 78:2179-2983.
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 2179-2983
-
-
Drew, H.R.1
Wing, R.M.2
Takano, T.3
Broka, C.4
Tanaka, S.5
Itikura, K.6
Dickerson, R.E.7
-
28
-
-
0027555852
-
Molecular dynamics simulations of B-DNA: An analysis of the role of initial molecular configuration, randomly assigned velocity distribution, long integration times, and nonconstrained termini
-
Falsafi, S., and N. O. Reich. 1993. Molecular dynamics simulations of B-DNA: an analysis of the role of initial molecular configuration, randomly assigned velocity distribution, long integration times, and nonconstrained termini. Biopolymers. 33:459-473.
-
(1993)
Biopolymers
, vol.33
, pp. 459-473
-
-
Falsafi, S.1
Reich, N.O.2
-
29
-
-
0023977089
-
The MIDAS display system
-
Ferrin, T. E., C. C. Huang, L. E. Jarvis, and R. Langridge. 1988. The MIDAS display system. J. Mol. Graph. 6:13-27.
-
(1988)
J. Mol. Graph.
, vol.6
, pp. 13-27
-
-
Ferrin, T.E.1
Huang, C.C.2
Jarvis, L.E.3
Langridge, R.4
-
30
-
-
0000857592
-
The structure of sodium thymo-nucleate fibers. I. the influence of water content
-
Franklin, R. E., and R. G. Gosling. 1953. The structure of sodium thymo-nucleate fibers. I. The influence of water content. Acta Crystallogr. 6:673-677.
-
(1953)
Acta Crystallogr.
, vol.6
, pp. 673-677
-
-
Franklin, R.E.1
Gosling, R.G.2
-
31
-
-
0021353172
-
Kinked DNA in crystalline complex with EcoRI endonuclease
-
Frederick, C. A., J. Grable, M. Melia, C. Samudzi, L. Jen-Jacobson, B.-C. Wang, P. Greene, H. W. Boyer, and J. M. Rosenberg. 1984. Kinked DNA in crystalline complex with EcoRI endonuclease. Nature. 309:327-330.
-
(1984)
Nature
, vol.309
, pp. 327-330
-
-
Frederick, C.A.1
Grable, J.2
Melia, M.3
Samudzi, C.4
Jen-Jacobson, L.5
Wang, B.-C.6
Greene, P.7
Boyer, H.W.8
Rosenberg, J.M.9
-
32
-
-
0028931709
-
B-DNA twisting correlates with base-pair morphology
-
Gorin, A. A., V. B. Zhurkin, and W. K. Olson. 1995. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:34-48.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 34-48
-
-
Gorin, A.A.1
Zhurkin, V.B.2
Olson, W.K.3
-
33
-
-
0028080634
-
Ab initio and molecular mechanics calculations on the hydrogen bond strengths in guanine-cytosine and adenine-thymine base pairs
-
Gould, I., and P. A. Kollman. 1993. Ab initio and molecular mechanics calculations on the hydrogen bond strengths in guanine-cytosine and adenine-thymine base pairs. J. Am. Chem. Soc. 116:2493-2494.
-
(1993)
J. Am. Chem. Soc.
, vol.116
, pp. 2493-2494
-
-
Gould, I.1
Kollman, P.A.2
-
34
-
-
0021179810
-
Two-fold symmetry of crystalline DNA-EcoRI endonuclease recognition complexes
-
Grable, J., C. A. Frederick, C. Samudzi, L. Jen Jacobson, D. Lesser, P. Greene, H. W. Boyer, K. Itakura, and J. M. Rosenberg. 1984. Two-fold symmetry of crystalline DNA-EcoRI endonuclease recognition complexes. J. Biomol. Struct. Dyn. 1:1149-1160.
-
(1984)
J. Biomol. Struct. Dyn.
, vol.1
, pp. 1149-1160
-
-
Grable, J.1
Frederick, C.A.2
Samudzi, C.3
Jen Jacobson, L.4
Lesser, D.5
Greene, P.6
Boyer, H.W.7
Itakura, K.8
Rosenberg, J.M.9
-
35
-
-
0021105577
-
Assignment of the non-exchangeable proton resonances of d(CGCGAATTCGCG) using 2D-NMR methods
-
Hare, D. R., D. E. Wemmer, S. H. Chou, G. Drobny, and B. R. Ried. 1983. Assignment of the non-exchangeable proton resonances of d(CGCGAATTCGCG) using 2D-NMR methods. J. Mol. Biol. 171:319-336.
-
(1983)
J. Mol. Biol.
, vol.171
, pp. 319-336
-
-
Hare, D.R.1
Wemmer, D.E.2
Chou, S.H.3
Drobny, G.4
Ried, B.R.5
-
36
-
-
84990406847
-
Dielectric effects in biopolymers: The theory of ionic saturation revisited
-
Hingerty, B. E., R. H. Ritchie, T. L. Ferrel, and J. E. Turner. 1985. Dielectric effects in biopolymers: the theory of ionic saturation revisited. Biopolymers. 24:427-439.
-
(1985)
Biopolymers
, vol.24
, pp. 427-439
-
-
Hingerty, B.E.1
Ritchie, R.H.2
Ferrel, T.L.3
Turner, J.E.4
-
37
-
-
84977299328
-
Anisotropic thermal parameter refinement of the DNA dodecamer CGCGAAT TCGCG by the segmented rigid body method
-
Holbrook, S. R., R. E. Dickerson, and S. H. Kim. 1985. Anisotropic thermal parameter refinement of the DNA dodecamer CGCGAAT TCGCG by the segmented rigid body method. Acta. Crystallogr. Sect. B. 41:255-262.
-
(1985)
Acta. Crystallogr. Sect. B.
, vol.41
, pp. 255-262
-
-
Holbrook, S.R.1
Dickerson, R.E.2
Kim, S.H.3
-
38
-
-
0026333329
-
Conic: A fast renderer for space-filling molecules with shadows
-
Huang, C. C., E. F. Pettersen, T. E. Klein, T. E. Ferrin, and R. Langridge. 1991. Conic: a fast renderer for space-filling molecules with shadows. J. Mol. Graph. 9:230-236.
-
(1991)
J. Mol. Graph.
, vol.9
, pp. 230-236
-
-
Huang, C.C.1
Pettersen, E.F.2
Klein, T.E.3
Ferrin, T.E.4
Langridge, R.5
-
39
-
-
0030763137
-
Localization of divalent metal ions in the minor groove of DNA A-tracts
-
Hud, N. V., and J. Feigon. 1997. Localization of divalent metal ions in the minor groove of DNA A-tracts. J. Am. Chem. Soc. 119:5756-5757.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 5756-5757
-
-
Hud, N.V.1
Feigon, J.2
-
40
-
-
0016266033
-
The B to A transition of DNA in solution
-
Ivanov, V. I., L. E. Minchenkova, E. E. Minyat, M. D. Frank-Kamentskii. and A. K. Schyolkina. 1974. The B to A transition of DNA in solution. J. Mol. Biol. 87:817-833.
-
(1974)
J. Mol. Biol.
, vol.87
, pp. 817-833
-
-
Ivanov, V.I.1
Minchenkova, L.E.2
Minyat, E.E.3
Frank-Kamentskii, M.D.4
Schyolkina, A.K.5
-
41
-
-
0024312492
-
Effect of crystal packing environment on conformation of the DNA duplex
-
Jain, S., and M. Sundaralingam. 1989. Effect of crystal packing environment on conformation of the DNA duplex. J. Biol. Chem. 264:12780-12784.
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 12780-12784
-
-
Jain, S.1
Sundaralingam, M.2
-
42
-
-
0024580271
-
The electrostatic potential of B-DNA
-
Jayaram, B., K. A. Sharp, and B. Honig. 1989. The electrostatic potential of B-DNA. Biopolymers. 28:975-993.
-
(1989)
Biopolymers
, vol.28
, pp. 975-993
-
-
Jayaram, B.1
Sharp, K.A.2
Honig, B.3
-
43
-
-
0025444642
-
Monte Carlo simulation studies of the structure of the counteranion atmosphere of B-DNA. Variations on the primitive dielectric model
-
Jayaram, B., S. Swaminathan, and D. L. Beveridge. 1990a. Monte Carlo simulation studies of the structure of the counteranion atmosphere of B-DNA. Variations on the primitive dielectric model. Macromolecules. 23:3156-3165.
-
(1990)
Macromolecules
, vol.23
, pp. 3156-3165
-
-
Jayaram, B.1
Swaminathan, S.2
Beveridge, D.L.3
-
44
-
-
0025444642
-
Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model
-
Jayaram, B., S. Swaminathan, D. L. Beveridge, K. Sharp, and B. Honig. 1990b. Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model. J. Phys. Chem. 23:3156-3165.
-
(1990)
J. Phys. Chem.
, vol.23
, pp. 3156-3165
-
-
Jayaram, B.1
Swaminathan, S.2
Beveridge, D.L.3
Sharp, K.4
Honig, B.5
-
45
-
-
33645858780
-
Transferable intermolecular potential functions for water, alcohols and ethers. Application to liquid water
-
Jorgensen, W. L. 1981. Transferable intermolecular potential functions for water, alcohols and ethers. Application to liquid water. J. Am. Chem. Soc. 103:335-340.
-
(1981)
J. Am. Chem. Soc.
, vol.103
, pp. 335-340
-
-
Jorgensen, W.L.1
-
46
-
-
0020692923
-
Ordered water structure around a B-DNA dodecamer: A qualitative study
-
Kopka, M. L., A. V. Fratini, H. R. Drew, and R. E. Dickerson. 1983. Ordered water structure around a B-DNA dodecamer: a qualitative 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
-
47
-
-
0002872006
-
The binding of netropsin to double helical DNA of sequence CGCGAATTCGCG: Single crystal x-ray structure analysis
-
Adenine Press, Guilderland, NY 461ff
-
Kopka, M. L., P. Pjura, C. Yoon, D. Goodsell, and R. E. Dickerson. 1985. The binding of netropsin to double helical DNA of sequence CGCGAATTCGCG: single crystal x-ray structure analysis. In Structure and Motion: Membranes, Nucleic Acids and Proteins. Adenine Press, Guilderland, NY. 461ff.
-
(1985)
Structure and Motion: Membranes, Nucleic Acids and Proteins
-
-
Kopka, M.L.1
Pjura, P.2
Yoon, C.3
Goodsell, D.4
Dickerson, R.E.5
-
48
-
-
0000235752
-
NMR evidence for DNA bound water in solution
-
Kubinec, M. G., and D. E. Wemmer. 1992. NMR evidence for DNA bound water in solution. J. Am. Chem. Soc. 114:8739-8740.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 8739-8740
-
-
Kubinec, M.G.1
Wemmer, D.E.2
-
49
-
-
0028578644
-
Molecular dynamics simulations suggest that the EcoRI kink is an example of molecular strain
-
Kumar, S., Y. Duan, P. A. Kollman, and J. M. Rosenberg. 1994. Molecular dynamics simulations suggest that the EcoRI kink is an example of molecular strain. J. Biomol. Struct. Dyn. 12:487-525.
-
(1994)
J. Biomol. Struct. Dyn.
, vol.12
, pp. 487-525
-
-
Kumar, S.1
Duan, Y.2
Kollman, P.A.3
Rosenberg, J.M.4
-
50
-
-
0025762608
-
Interaction of Berenil with the EcoRI dodecamer d(CGCGAATTCGCG) in solution studied by NMR
-
Lane, A., T. C. Jenkins, T. Brown, and S. Neidle. 1991. Interaction of Berenil with the EcoRI dodecamer d(CGCGAATTCGCG) in solution studied by NMR. Biochemistry. 30:1372-1385.
-
(1991)
Biochemistry
, vol.30
, pp. 1372-1385
-
-
Lane, A.1
Jenkins, T.C.2
Brown, T.3
Neidle, S.4
-
52
-
-
0022008114
-
The dependence of the surface electrostatic potential of B-DNA on environmental factors
-
Lavery, R., and B. Pullman. 1985. The dependence of the surface electrostatic potential of B-DNA on environmental factors. J. Biomol. Struct. Dyn. 5:1021-32.
-
(1985)
J. Biomol. Struct. Dyn.
, vol.5
, pp. 1021-1032
-
-
Lavery, R.1
Pullman, B.2
-
53
-
-
0024058085
-
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
-
Lavery, R., and H. Sklenar. 1988. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6:63-91.
-
(1988)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, A.H.2
-
54
-
-
13144289494
-
Curves 51 - Helical analysis of irregular nucleic acids
-
Institut de Biologie Physico-Chimique, Paris
-
Lavery, R., and H. Sklenar. 1996. Curves 51 - helical analysis of irregular nucleic acids. Laboratoire de Biochimie Theorique, CNRS URA 77. Institut de Biologie Physico-Chimique, Paris.
-
(1996)
Laboratoire de Biochimie Theorique, CNRS URA
, vol.77
-
-
Lavery, R.1
Sklenar, H.2
-
55
-
-
0027058824
-
NMR observation of individual molecules of hydration water bound to DNA duplexes: Direct evidence for a spine of hydration water present in aqueous solution
-
Liepinsh, E., G. Otting, and K. Wüthrich. 1992. NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution. Nucleic Acids Res. 20:6549-6553.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 6549-6553
-
-
Liepinsh, E.1
Otting, G.2
Wüthrich, K.3
-
56
-
-
0024795316
-
The effects of truncating long-range forces on protein dynamics
-
Loncharich, R. J., and B. R. Brooks. 1989. The effects of truncating long-range forces on protein dynamics. Proteins. 6:32-45.
-
(1989)
Proteins
, vol.6
, pp. 32-45
-
-
Loncharich, R.J.1
Brooks, A.B.R.2
-
58
-
-
6344260593
-
An all-atom empirical energy function for the simulation of nucleic acids
-
Mackerell, A. D., Jr., T. Wiorkiewicz-Kuizera, and M. Karplus. 1995. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:11946-11975.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 11946-11975
-
-
Mackerell Jr., A.D.1
Wiorkiewicz-Kuizera, T.2
Karplus, M.3
-
59
-
-
0017895903
-
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
-
Manning, G. S. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11:179-246.
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 179-246
-
-
Manning, G.S.1
-
60
-
-
0028052906
-
A nanosecond molecular dynamics trajectory for a B DNA double helix: Evidence for substates
-
McConnell, K. M., R. Nirmala, M. A. Young, G. Ravishanker, and D. L. Beveridge. 1994. A nanosecond molecular dynamics trajectory for a B DNA double helix: evidence for substates. J. Am. Chem. Soc. 116:4461-4462.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 4461-4462
-
-
McConnell, K.M.1
Nirmala, R.2
Young, M.A.3
Ravishanker, G.4
Beveridge, D.L.5
-
62
-
-
0022462967
-
Structural chemistry of biomolecular hydration: The proximity criterion
-
Mezei, M., and D. L. Beveridge. 1986. Structural chemistry of biomolecular hydration: the proximity criterion. Methods Enzymol. 127:21-47.
-
(1986)
Methods Enzymol
, vol.127
, pp. 21-47
-
-
Mezei, M.1
Beveridge, D.L.2
-
63
-
-
0029804674
-
Computational simulations of DNA distortions by a syn, cis cyclobutane thymine dimer lesion
-
Miaskiewicz, K., J. Miller, M. Cooney, and R. Osman. 1996. Computational simulations of DNA distortions by a syn, cis cyclobutane thymine dimer lesion. J. Am. Chem. Soc. 118:9156-9163.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 9156-9163
-
-
Miaskiewicz, K.1
Miller, J.2
Cooney, M.3
Osman, R.4
-
64
-
-
0000935991
-
Molecular dynamics simulation of the hydrated d(CGCGAATTCGCG)2 dodecamer
-
Miaskiewicz, K., R. Osman, and H. Weinstein. 1993. Molecular dynamics simulation of the hydrated d(CGCGAATTCGCG)2 dodecamer. J. Am. Chem. Soc. 115:1526-1537.
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 1526-1537
-
-
Miaskiewicz, K.1
Osman, R.2
Weinstein, H.3
-
65
-
-
0025194337
-
Proton exchange and base-pair opening kinetics in 5′-d(CGCGAATTCGCG)-3′ and related dodecamers
-
Moe, J. G., and I. M. Russu. 1990. Proton exchange and base-pair opening kinetics in 5′-d(CGCGAATTCGCG)-3′ and related dodecamers. Nucleic Acids Res. 18:821-827.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 821-827
-
-
Moe, J.G.1
Russu, I.M.2
-
66
-
-
0026737976
-
Kinetics and energetics of base-pair opening in 5′-d(CGCGAATTCGCG)-3′ and a substituted dodecamer containing GT mismatches
-
Moe, J. G., and I. M. Russu. 1992. Kinetics and energetics of base-pair opening in 5′-d(CGCGAATTCGCG)-3′ and a substituted dodecamer containing GT mismatches. Biochemistry. 31:8421-8428.
-
(1992)
Biochemistry
, vol.31
, pp. 8421-8428
-
-
Moe, J.G.1
Russu, I.M.2
-
67
-
-
0025787463
-
Crystal and molecular structure of a DNA fragment: D(CGTGAATTCACG)
-
Narayana, N., S. L. Ginell, I. M. Russu, and H. M. Berman. 1991. Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG). Biochemistry. 30:4449-4455.
-
(1991)
Biochemistry
, vol.30
, pp. 4449-4455
-
-
Narayana, N.1
Ginell, S.L.2
Russu, I.M.3
Berman, H.M.4
-
68
-
-
0024788819
-
Solution structure of the EcoRI DNA sequence: Refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations
-
Nerdal, W., D. R. Hare, and B. R. Reid. 1989. Solution structure of the EcoRI DNA sequence: refinement of NMR-derived distance geometry structures by NOESY spectrum back-calculations. Biochemistry. 28:10008-10021.
-
(1989)
Biochemistry
, vol.28
, pp. 10008-10021
-
-
Nerdal, W.1
Hare, D.R.2
Reid, B.R.3
-
69
-
-
0027772178
-
Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine
-
Nunn, C. M., T. C. Jenkins, and S. Neidle. 1993. Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine. Biochemistry. 32:13838-13843.
-
(1993)
Biochemistry
, vol.32
, pp. 13838-13843
-
-
Nunn, C.M.1
Jenkins, T.C.2
Neidle, S.3
-
70
-
-
0026253640
-
Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysis
-
Olmsted, M. C., C. F. Anderson, and M. T. Record, Jr. 1991. Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: a grand canonical Monte Carlo analysis. Biopolymers. 31:1593-1604.
-
(1991)
Biopolymers
, vol.31
, pp. 1593-1604
-
-
Olmsted, M.C.1
Anderson, C.F.2
Record Jr., M.T.3
-
71
-
-
0345108269
-
Theoretical studies of nucleic acid conformation: Potential energies, chain statistics, and model building
-
MacMillan, London
-
Olson, W. 1982a. Theoretical studies of nucleic acid conformation: potential energies, chain statistics, and model building. In Topics in Nucleic Acid Structure. MacMillan, London. 1-79.
-
(1982)
Topics in Nucleic Acid Structure
, pp. 1-79
-
-
Olson, W.1
-
72
-
-
0019923858
-
How flexible is the furanose ring? An updated potential energy estimate
-
Olson, W. K. 1982b. How flexible is the furanose ring? An updated potential energy estimate. J. Am. Chem. Soc. 104:278-286.
-
(1982)
J. Am. Chem. Soc.
, vol.104
, pp. 278-286
-
-
Olson, W.K.1
-
74
-
-
0001200839
-
Phosphorous NMR spectral analysis of the dodecamer d(CGCGAATTCGCG)
-
Ott, J., and F. Eckstein. 1985. Phosphorous NMR spectral analysis of the dodecamer d(CGCGAATTCGCG). Biochemistry. 24:2530-2535.
-
(1985)
Biochemistry
, vol.24
, pp. 2530-2535
-
-
Ott, J.1
Eckstein, F.2
-
75
-
-
0020473197
-
Premelting and melting transitions in the d(CGCGAATTCGCG) self-complementary duplex in solution
-
Patel, D. J., S. A. Kozlowski, L. A. Marky, C. Broka, J. A. Rice, K. Itakura, and K. J. Breslauer. 1982. Premelting and melting transitions in the d(CGCGAATTCGCG) self-complementary duplex in solution. Biochemistry. 21:428-436.
-
(1982)
Biochemistry
, vol.21
, pp. 428-436
-
-
Patel, D.J.1
Kozlowski, S.A.2
Marky, L.A.3
Broka, C.4
Rice, J.A.5
Itakura, K.6
Breslauer, K.J.7
-
76
-
-
0004023361
-
-
University of California, San Francisco, CA
-
Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, III, D. M. Fergusen, G. L. Seibel, U. C. Singh, P. Weiner, and P. Kollman. 1995. AMBER 41. University of California, San Francisco, CA.
-
(1995)
AMBER
, vol.41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham III, T.E.5
Fergusen, D.M.6
Seibel, G.L.7
Singh, U.C.8
Weiner, P.9
Kollman, P.10
-
77
-
-
0024291323
-
Structural modeling of the distamycin A-d(CGCGAATTCGCG)2 complex using 2D NMR and molecular mechanics
-
Pelton, J. G., and D. E. Wemmer. 1988. Structural modeling of the distamycin A-d(CGCGAATTCGCG)2 complex using 2D NMR and molecular mechanics. Biochemistry. 27:8088-8096.
-
(1988)
Biochemistry
, vol.27
, pp. 8088-8096
-
-
Pelton, J.G.1
Wemmer, D.E.2
-
79
-
-
0027561360
-
Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: Application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2
-
Prevost, C., S. Louise May, G. Ravishanker, R. Lavery, and D. L. Beveridge. 1993. Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers. 33:335-350.
-
(1993)
Biopolymers
, vol.33
, pp. 335-350
-
-
Prevost, C.1
Louise May, S.2
Ravishanker, G.3
Lavery, R.4
Beveridge, D.L.5
-
80
-
-
33845790250
-
Molecular dynamics study of liquid water
-
Rahman, A., and F. H. Stillinger. 1971. Molecular dynamics study of liquid water. J. Chem. Phys. 55:3336-3359.
-
(1971)
J. Chem. Phys.
, vol.55
, pp. 3336-3359
-
-
Rahman, A.1
Stillinger, F.H.2
-
81
-
-
0025264049
-
Simulations of the B-DNA molecular dynamics of d(CGCGAATTCGCG)2 and d(GCGCGCGCGC)2: An analysis of the role of initial geometry and a comparison of united and all-atom models
-
Rao, S. N., and P. Kollman. 1990. Simulations of the B-DNA molecular dynamics of d(CGCGAATTCGCG)2 and d(GCGCGCGCGC)2: an analysis of the role of initial geometry and a comparison of united and all-atom models. Biopolymers. 29:517-532.
-
(1990)
Biopolymers
, vol.29
, pp. 517-532
-
-
Rao, S.N.1
Kollman, P.2
-
82
-
-
0031516150
-
Treatment of Counterions in Computer Simulations of DNA
-
Ravishanker, G., P. Auffinger, D. R. Langley, B. Jayaram, M. A. Young, and D. L. Beveridge. 1997. Treatment of Counterions in Computer Simulations of DNA. In Reviews in Computational Chemistry. 11:317-372.
-
(1997)
Reviews in Computational Chemistry
, vol.11
, pp. 317-372
-
-
Ravishanker, G.1
Auffinger, P.2
Langley, D.R.3
Jayaram, B.4
Young, M.A.5
Beveridge, D.L.6
-
84
-
-
0024556774
-
Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves," dials and windows
-
Ravishanker, G., S. Swaminathan, D. L. Beveridge, R. Lavery, and H. Sklenar. 1989. Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves," dials and windows. J. Biomol. Struct. Dyn. 6:669-699.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 669-699
-
-
Ravishanker, G.1
Swaminathan, S.2
Beveridge, D.L.3
Lavery, R.4
Sklenar, H.5
-
86
-
-
0028823008
-
Hydration of the DNA bases is local
-
Schneider, B., and H. M. Berman. 1995. Hydration of the DNA bases is local. Biophys. J. 69:2661-2669.
-
(1995)
Biophys. J.
, vol.69
, pp. 2661-2669
-
-
Schneider, B.1
Berman, H.M.2
-
87
-
-
0026896780
-
Hydration of DNA bases: Analysis of crystallographic data
-
Schneider, B., D. Cohen, and H. M. Bennan. 1992. Hydration of DNA bases: analysis of crystallographic data. Biopolymers. 32:725-750.
-
(1992)
Biopolymers
, vol.32
, pp. 725-750
-
-
Schneider, B.1
Cohen, D.2
Bennan, H.M.3
-
88
-
-
0027138869
-
A systematic method for studying the spatial distribution of water molecules around nucleic acid bases
-
Schneider, B., D. M. Cohen, L. Schleifer, A. R. Srinivasan, W. K. Olson, and H. M. Berman. 1993. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys. J. 65:2291-2303.
-
(1993)
Biophys. J.
, vol.65
, pp. 2291-2303
-
-
Schneider, B.1
Cohen, D.M.2
Schleifer, L.3
Srinivasan, A.R.4
Olson, W.K.5
Berman, H.M.6
-
89
-
-
84965102253
-
RNA double-helical fragments at atomic resolution. I. the crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate
-
Seeman, N. C., J. M. Rosenberg, F. L. Suddath, J. J. P. Kim, and A. Rich. 1976. RNA double-helical fragments at atomic resolution. I. The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate. J. Mol. Biol. 104:109-144.
-
(1976)
J. Mol. Biol.
, vol.104
, pp. 109-144
-
-
Seeman, N.C.1
Rosenberg, J.M.2
Suddath, F.L.3
Kim, J.J.P.4
Rich, A.5
-
90
-
-
0024462296
-
The conformation of the DNA double helix in the crystal is dependent on its environment
-
Shakked, Z., G. Guerstein Guzikevich, M. Eisenstein, F. Frolow, and D. Rabinovich. 1989. The conformation of the DNA double helix in the crystal is dependent on its environment. Nature. 342:456-460.
-
(1989)
Nature
, vol.342
, pp. 456-460
-
-
Shakked, Z.1
Guerstein Guzikevich, G.2
Eisenstein, M.3
Frolow, F.4
Rabinovich, D.5
-
91
-
-
26744435700
-
Peptides in ionic solutions: A comparison of the Ewald and switching function techniques
-
Smith, P. E., and B. M. Pettitt. 1991. Peptides in ionic solutions: a comparison of the Ewald and switching function techniques. J. Chem. Phys. 95:8430-8441.
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 8430-8441
-
-
Smith, P.E.1
Pettitt, B.M.2
-
92
-
-
0000112790
-
Ewald artifacts in liquid state molecular dynamics simulations
-
Smith, P. E., and B. M. Pettitt. 1996. Ewald artifacts in liquid state molecular dynamics simulations. J. Chem. Phys. 105:4289-4293.
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 4289-4293
-
-
Smith, P.E.1
Pettitt, B.M.2
-
93
-
-
0025112951
-
Molecular dynamics of an in vacuo model of duplex d(CGCGAATTCGCG) in the B-form based on the amber 30 force field
-
Srinivasan, J., J. M. Withka, and D. L. Beveridge. 1990. Molecular dynamics of an in vacuo model of duplex d(CGCGAATTCGCG) in the B-form based on the amber 30 force field. Biophys. J. 58:533-547.
-
(1990)
Biophys. J.
, vol.58
, pp. 533-547
-
-
Srinivasan, J.1
Withka, J.M.2
Beveridge, D.L.3
-
94
-
-
84986534166
-
New spherical-cutoff methods for long-range forces in macromolecular simulation
-
Steinbach, P. J., and B. R. Brooks. 1994. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comp. Chem. 15:667-683.
-
(1994)
J. Comp. Chem.
, vol.15
, pp. 667-683
-
-
Steinbach, P.J.1
Brooks, B.R.2
-
95
-
-
0025280401
-
Structural studies of protein-nucleic acid interactions: The sources of sequence-specific binding
-
Steitz, T. A. 1990. Structural studies of protein-nucleic acid interactions: the sources of sequence-specific binding. Q. Rev. Biophys. 23:205-280.
-
(1990)
Q. Rev. Biophys.
, vol.23
, pp. 205-280
-
-
Steitz, T.A.1
-
96
-
-
0028184697
-
Measuring the geometry of DNA grooves
-
Stofer, E., and R. Lavery. 1994. Measuring the geometry of DNA grooves. Biopolymers. 34:337-346.
-
(1994)
Biopolymers.
, vol.34
, pp. 337-346
-
-
Stofer, E.1
Lavery, R.2
-
97
-
-
0024678912
-
A theoretical study of the aqueous hydration of canonical B d(CGCGAATTCGCG): Monte Carlo simulation and comparison with crystallographic ordered water sites
-
Subramanian, P. S., and D. L. Beveridge. 1989. A theoretical study of the aqueous hydration of canonical B d(CGCGAATTCGCG): Monte Carlo simulation and comparison with crystallographic ordered water sites. J. Biomol. Struct. Dyn. 6:1093-1122.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 1093-1122
-
-
Subramanian, P.S.1
Beveridge, D.L.2
-
98
-
-
0024121512
-
Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG)d(GCGCTTAAGCGC): Monte Carlo computer simulation
-
Subramanian, P. S., G. Ravishanker, and D. L. Beveridge. 1988. Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG)d(GCGCTTAAGCGC): Monte Carlo computer simulation. Proc. Natl. Acad. Sci. USA. 85:1836-1840.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 1836-1840
-
-
Subramanian, P.S.1
Ravishanker, G.2
Beveridge, D.L.3
-
99
-
-
0025338247
-
Theoretical account of the "spine of hydration" in the minor groove of duplex d(CGCGAATTCGCG)
-
Subramanian, P. S., S. Swaminathan, and D. L. Beveridge. 1990. Theoretical account of the "spine of hydration" in the minor groove of duplex d(CGCGAATTCGCG). J. Biomol. Struct. Dyn. 7:1161-1165.
-
(1990)
J. Biomol. Struct. Dyn.
, vol.7
, pp. 1161-1165
-
-
Subramanian, P.S.1
Swaminathan, S.2
Beveridge, D.L.3
-
100
-
-
0010667559
-
A theoretical study of the structure of liquid water based on quasicomponent distribution functions
-
Swaminathan, S., and D. L. Beveridge. 1977. A theoretical study of the structure of liquid water based on quasicomponent distribution functions. J. Am. Chem. Soc. 99:8392-8398.
-
(1977)
J. Am. Chem. Soc.
, vol.99
, pp. 8392-8398
-
-
Swaminathan, S.1
Beveridge, A.D.L.2
-
101
-
-
0000930430
-
Molecular dynamics of B-DNA including water and counterions: A 140 ps trajectory for d(CGCGAATTCGCG) based on the GROMOS force field
-
Swaminathan, S., G. Ravishanker, and D. L. Beveridge. 1991. Molecular dynamics of B-DNA including water and counterions: a 140 ps trajectory for d(CGCGAATTCGCG) based on the GROMOS force field. J. Am. Chem. Soc. 111:5027-5040.
-
(1991)
J. Am. Chem. Soc.
, vol.111
, pp. 5027-5040
-
-
Swaminathan, S.1
Ravishanker, G.2
Beveridge, D.L.3
-
102
-
-
84987068914
-
Ewald summation retards translational motion in molecular dynamics simulation in water
-
Teleman, O., and A. Wallqvist. 1990. Ewald summation retards translational motion in molecular dynamics simulation in water. Int. J. Quant. Chem. Quant. Chem. Symp. 24:245-249.
-
(1990)
Int. J. Quant. Chem. Quant. Chem. Symp.
, vol.24
, pp. 245-249
-
-
Teleman, O.1
Wallqvist, A.2
-
103
-
-
0024296533
-
The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG)
-
Teng, M.-K., N. Usman, C. A. Frederick, and A. H.-J. Wang. 1988. The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucleic Acids Res. 16:2671-2690.
-
(1988)
Nucleic Acids Res.
, vol.16
, pp. 2671-2690
-
-
Teng, M.-K.1
Usman, N.2
Frederick, C.A.3
Wang, A.H.-J.4
-
104
-
-
0021677578
-
Large amplitude bending motions in phenylalanine transfer RNA
-
Tung, S. C., S. C. Harvey, and A. J. McCammon. 1984. Large amplitude bending motions in phenylalanine transfer RNA. Biopolymers. 23:2173-2193.
-
(1984)
Biopolymers
, vol.23
, pp. 2173-2193
-
-
Tung, S.C.1
Harvey, S.C.2
McCammon, A.J.3
-
106
-
-
0023423078
-
Sequence dependent conformation of oligomeric DNAs in aqueous solution and in crystals
-
Wang, Y., G. A. Thomas, and W. Peticolas. 1987. Sequence dependent conformation of oligomeric DNAs in aqueous solution and in crystals. J. Biomol. Struct. Dyn. 5:249-274.
-
(1987)
J. Biomol. Struct. Dyn.
, vol.5
, pp. 249-274
-
-
Wang, Y.1
Thomas, G.A.2
Peticolas, W.3
-
107
-
-
0025083328
-
A Raman study of low frequency intrahelical modes in A-, B-, and C-DNA
-
Weidlich, T., S. M. Lindsay, Q. Rui, A. Rupprecht, W. L. Peticolas, and G. A. Thomas. 1990. A Raman study of low frequency intrahelical modes in A-, B-, and C-DNA. J. Biomol. Struct. Dyn. 8:139-171.
-
(1990)
J. Biomol. Struct. Dyn.
, vol.8
, pp. 139-171
-
-
Weidlich, T.1
Lindsay, S.M.2
Rui, Q.3
Rupprecht, A.4
Peticolas, W.L.5
Thomas, G.A.6
-
108
-
-
0021757436
-
A new force field for molecular mechanical simulations of proteins and nucleic acids
-
Weiner, S. J., P. Kollman, D. A. Case, C. U. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner. 1984. A new force field for molecular mechanical simulations of proteins and nucleic acids. J. Am. Chem. Soc. 106:765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.2
Case, D.A.3
Singh, C.U.4
Ghio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.8
-
109
-
-
84988053694
-
An all atom force field for simulations of proteins and nucleic acids
-
Weiner, S. J., P. A. Kollman, D. T. Nguyen, and D. A. Case. 1986. An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:230-238.
-
(1986)
J. Comp. Chem.
, vol.7
, pp. 230-238
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
112
-
-
0019331504
-
Crystal structure analysis of a complete turn of B-DNA
-
Wing, R. M., H. R. Drew, T. Takano, C. Broka, S. Tanaka, I. Itakura, and R. E. Dickerson. 1980. Crystal structure analysis of a complete turn of B-DNA. Nature. 287:755-758.
-
(1980)
Nature
, vol.287
, pp. 755-758
-
-
Wing, R.M.1
Drew, H.R.2
Takano, T.3
Broka, C.4
Tanaka, S.5
Itakura, I.6
Dickerson, R.E.7
-
113
-
-
0026511587
-
Toward a dynamical structure of DNA: Comparison of theoretical and experimental NOE intensities
-
Withka, J. M., S. Swaminathan, J. Srinivasan, D. L. Beveridge, and P. H. Bolton. 1992. Toward a dynamical structure of DNA: comparison of theoretical and experimental NOE intensities. Science. 255:597-599.
-
(1992)
Science
, vol.255
, pp. 597-599
-
-
Withka, J.M.1
Swaminathan, S.2
Srinivasan, J.3
Beveridge, D.L.4
Bolton, P.H.5
-
114
-
-
0016742396
-
Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. the role of hydration
-
Wolf, B., and S. Hanlon. 1975. Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration. Biochemistry. 14:1661-1670.
-
(1975)
Biochemistry
, vol.14
, pp. 1661-1670
-
-
Wolf, B.1
Hanlon, S.2
-
115
-
-
33748674257
-
B to A transition of DNA on the nanosecond timescale
-
Yang, Y., and B. M. Pettitt. 1996. B to A transition of DNA on the nanosecond timescale. J. Phys. Chem. 100:2564-2566.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2564-2566
-
-
Yang, Y.1
Pettitt, B.M.2
-
116
-
-
36449007976
-
The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
-
York, D. M., T. A. Darden, and L. G. Pedersen. 1993. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys. 99:8345-8348.
-
(1993)
J. Chem. Phys.
, vol.99
, pp. 8345-8348
-
-
York, D.M.1
Darden, T.A.2
Pedersen, L.G.3
-
117
-
-
0028068802
-
Atomic-level accuracy in simulations of large protein crystals
-
York, D. M., A. Wlodawer, L. G. Pedersen, and T. A. Darden. 1994. Atomic-level accuracy in simulations of large protein crystals. Proc. Natl. Acad. Sci. USA. 91:8715-8718.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 8715-8718
-
-
York, D.M.1
Wlodawer, A.2
Pedersen, L.G.3
Darden, T.A.4
-
118
-
-
0029110156
-
Toward the accurate modeling of DNA: The importance of long-range electrostatics
-
York, D. M., W. Yang, H. Lee, T. Darden, and L. G. Pedersen. 1995. Toward the accurate modeling of DNA: the importance of long-range electrostatics. J. Am. Chem. Soc. 117:5001-5002.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5001-5002
-
-
York, D.M.1
Yang, W.2
Lee, H.3
Darden, T.4
Pedersen, L.G.5
-
119
-
-
0031047279
-
Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
-
Young, M. A., B. Jayaram, and D. L. Beveridge. 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
Jayaram, B.2
Beveridge, D.L.3
-
120
-
-
0001552411
-
Analysis of helix bending in crystal structures and molecular dynamics simulations of DNA oligonucleotides
-
Structural Biology: The State of the Art. Adenine Press, Albany, NY
-
Young, M. A., R. Nirmala, J. Srinivasan, K. J. McConnell, G. Ravishanker, D. L. Beveridge, and H. M. Berman. 1994. Analysis of helix bending in crystal structures and molecular dynamics simulations of DNA oligonucleotides. In Structural Biology: The State of the Art. Proceedings of the 8th Conversation. Adenine Press, Albany, NY. 197-214.
-
(1994)
Proceedings of the 8th Conversation
, pp. 197-214
-
-
Young, M.A.1
Nirmala, R.2
Srinivasan, J.3
McConnell, K.J.4
Ravishanker, G.5
Beveridge, D.L.6
Berman, H.M.7
-
121
-
-
0029006896
-
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes
-
Young, M. A., G. Ravishanker, D. L. Beveridge, and H. M. Berman. 1995a. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes, Biophys. J. 68:2454-2468.
-
(1995)
Biophys. J.
, vol.68
, pp. 2454-2468
-
-
Young, M.A.1
Ravishanker, G.2
Beveridge, D.L.3
Berman, H.M.4
-
122
-
-
0028850111
-
Structure determination and analysis of local bending in an A-tract DNA duplex: Comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG)
-
Young, M. A., J. Srinivasan, I. Goljer, S. Kumar, D. L. Beveridge, and P. H. Bolton. 1995b. Structure determination and analysis of local bending in an A-tract DNA duplex: comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG). Methods Enzymol. 261:121-144.
-
(1995)
Methods Enzymol
, vol.261
, pp. 121-144
-
-
Young, M.A.1
Srinivasan, J.2
Goljer, I.3
Kumar, S.4
Beveridge, D.L.5
Bolton, P.H.6
|