-
2
-
-
0000946971
-
Atomic coordinates and molecular conformations for DNA-DNA, RNA-RNA and DNA-RNA helices
-
(Fasman, G. D., ed.), CRC Press Inc., Cleveland
-
Arnott, S., Campbell-Smith, P. & Chandrasekaran, R. (1976). Atomic coordinates and molecular conformations for DNA-DNA, RNA-RNA and DNA-RNA helices. In C.R.C. Handbook of Biochemistry and Molecular Biology (Fasman, G. D., ed.), pp. 411-422, CRC Press Inc., Cleveland.
-
(1976)
C.R.C. Handbook of Biochemistry and Molecular Biology
, pp. 411-422
-
-
Arnott, S.1
Campbell-Smith, P.2
Chandrasekaran, R.3
-
3
-
-
0028221654
-
The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters
-
Babcock, M. S. & Olson, W. K. (1994). The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters. J. Mol. Biol. 237, 98-124.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 98-124
-
-
Babcock, M.S.1
Olson, W.K.2
-
4
-
-
0011219597
-
Dynamic structure of proteins in solution-comparison of theoretical and experimental NMR parameters of BPTI
-
Balasubramanian, S., Nirmala, R., Beveridge, D. L. & Bolton, P. H. (1993). Dynamic structure of proteins in solution-comparison of theoretical and experimental NMR parameters of BPTI. J. Cell. Biochem. 289.
-
(1993)
J. Cell. Biochem.
, pp. 289
-
-
Balasubramanian, S.1
Nirmala, R.2
Beveridge, D.L.3
Bolton, P.H.4
-
5
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. J. Comput. Phys. 81, 3684-3690.
-
(1984)
J. Comput. 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
-
7
-
-
0028241354
-
Hydration of DNA: Take 2
-
Berman, H. M. (1994). Hydration of DNA: take 2. Curr. Opin. Struct. Biol. 4, 345-350.
-
(1994)
Curr. Opin. Struct. Biol.
, vol.4
, pp. 345-350
-
-
Berman, H.M.1
-
8
-
-
0023985712
-
A systematic study of patterns of hydration in nucleic acids: (I) guanine and cytosine
-
Berman, H. M., Sowri, A., Ginell, S. & Beveridge, D. L. (1988). A systematic study of patterns of hydration in nucleic acids: (I) guanine and cytosine. J. Biomol. Struct. Dynam. 5, 1101-1110.
-
(1988)
J. Biomol. Struct. Dynam.
, vol.5
, pp. 1101-1110
-
-
Berman, H.M.1
Sowri, A.2
Ginell, S.3
Beveridge, D.L.4
-
10
-
-
0011156533
-
Molecular simulation studies on the d(CGCGAATTCGCG) duplex: Hydration, ion atomosphere, structure and dynamics
-
Beveridge, D. L., Subramanian, P., Jayaram, B., Swaminathan, S. & Ravishanker, G. (1990). Molecular simulation studies on the d(CGCGAATTCGCG) duplex: hydration, ion atomosphere, structure and dynamics. J. Biomol. Struct. Dynam. 3, 79-112.
-
(1990)
J. Biomol. Struct. Dynam.
, vol.3
, pp. 79-112
-
-
Beveridge, D.L.1
Subramanian, P.2
Jayaram, B.3
Swaminathan, S.4
Ravishanker, G.5
-
11
-
-
0002593973
-
Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers
-
(Westhof, E., ed.), The Macmillan Press Ltd, London
-
Beveridge, D. L., Swaminathan, S., Ravishankar, G., Withka, J. M., Srinivasan, J, Prevost, C., Louise-May, S., Langley, D. R., DiCapua, F. M. & Bolton, P. H. (1993). Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers. In Water and Biological Macromolecules (Westhof, E., ed.), pp. 166-225, The Macmillan Press Ltd, London.
-
(1993)
Water and Biological Macromolecules
, pp. 166-225
-
-
Beveridge, D.L.1
Swaminathan, S.2
Ravishankar, 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
-
12
-
-
0028913948
-
Solution structure of an oncogenic DNA duplex, the K-ras gene and the sequence containing a central CA or AG mismatch as a function of pH: Nuclear magnetic resonance and molecular dynamics studies
-
Boulard, Y., Cognet, J. A. H., Gabarro-Arpa, J., Le Bret, M., Carbonnaux, C. & Fazakerley, G. V. (1995). Solution structure of an oncogenic DNA duplex, the K-ras gene and the sequence containing a central CA or AG mismatch as a function of pH: nuclear magnetic resonance and molecular dynamics studies. J. Mol. Biol, 246, 194-208.
-
(1995)
J. Mol. Biol
, vol.246
, pp. 194-208
-
-
Boulard, Y.1
Cognet, J.A.H.2
Gabarro-Arpa, J.3
Le Bret, M.4
Carbonnaux, C.5
Fazakerley, G.V.6
-
13
-
-
0003525155
-
-
John Wiley & Sons, New York
-
Brooks, C. L., III, Karplus, M. & Pettitt, B. M. (1989). Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. John Wiley & Sons, New York.
-
(1989)
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
-
-
Brooks C.L. III1
Karplus, M.2
Pettitt, B.M.3
-
14
-
-
0023140814
-
Crystalographic R-factor refinement by molecular dynamics
-
Brunger, A., Kuriyan, J. & Karplus, M. (1987). Crystalographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
-
(1987)
Science
, vol.235
, pp. 458-460
-
-
Brunger, A.1
Kuriyan, J.2
Karplus, M.3
-
15
-
-
0029941154
-
Observation of the A-DNA and B-DNA transition during unrestrained molecular dynamics in aqueous solution
-
Cheatham, T. E., III & Kollman, P. A. (1996). Observation of the A-DNA and 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 T.E. III1
Kollman, P.A.2
-
16
-
-
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, Miller, J. L., Fox, T., Darden, T. A. & Kollman, P. A. (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 T.E. III1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
17
-
-
0027315767
-
Synergistic effects in the melting of DNA hydration shell: Melting of the minor groove hydration spine in poly (dA)·poly(dT) and its effect on base pair stability
-
Chen, Y. Z. & Prohofsky, E. W. (1993). Synergistic effects in the melting of DNA hydration shell: melting of the minor groove hydration spine in poly (dA)·poly(dT) and its effect on base pair stability. Biophys. J. 64, 1385-1393.
-
(1993)
Biophys. J.
, vol.64
, pp. 1385-1393
-
-
Chen, Y.Z.1
Prohofsky, E.W.2
-
18
-
-
0028218497
-
Premelting base pair opening probability and drug binding constant of a daunomycin-poly d(GCAT)·poly d(ATGC) complex
-
Chen, Y. Z. & Prohofsky, E. W. (1994). Premelting base pair opening probability and drug binding constant of a daunomycin-poly d(GCAT)·poly d(ATGC) complex. Biophys. J. 66, 820-826.
-
(1994)
Biophys. J.
, vol.66
, pp. 820-826
-
-
Chen, Y.Z.1
Prohofsky, E.W.2
-
19
-
-
85030306195
-
The integration of recognition and cleavage: X-ray structure of substrate-and product-containing DNA-EcoRI endonuclease complex
-
In the press
-
Choi, J., Kim, Y., Chandrasekhar, K., Wilkosz, P. A., Grable, J. C., Greene, P., Hager, P. & Rosenberg, J. M. (1997). The integration of recognition and cleavage: X-ray structure of substrate-and product-containing DNA-EcoRI endonuclease complex. Proteins: Struct. Funct. Genet. In the press.
-
(1997)
Proteins: Struct. Funct. Genet.
-
-
Choi, J.1
Kim, Y.2
Chandrasekhar, K.3
Wilkosz, P.A.4
Grable, J.C.5
Greene, P.6
Hager, P.7
Rosenberg, J.M.8
-
20
-
-
0026019603
-
Molecular dynamics simulation of the hydration shell of a B-DNA decamer reveals two main types of minor-groove hydration depending on groove width
-
Chuprina, V. P., Heinemann, U., Nurislamov, A. A., Zielenkiewicz, P., Dickerson, R. E. & Saenger, W. (1991). Molecular dynamics simulation of the hydration shell of a B-DNA decamer reveals two main types of minor-groove hydration depending on groove width. Proc. Natl Acad. Sci. USA, 88, 593-597.
-
(1991)
Proc. Natl Acad. Sci. USA
, vol.88
, pp. 593-597
-
-
Chuprina, V.P.1
Heinemann, U.2
Nurislamov, A.A.3
Zielenkiewicz, P.4
Dickerson, R.E.5
Saenger, W.6
-
21
-
-
0028928438
-
Helical parameters, fluctuations, alternative hydrogen bonding, and bending in oligonucleotides containing a mismatched base-pair by NOESY distance restrained and distance free molecular dynamics
-
Cognet, J. A. H., Boulard, Y & Fazakerley, G. V. (1995). Helical parameters, fluctuations, alternative hydrogen bonding, and bending in oligonucleotides containing a mismatched base-pair by NOESY distance restrained and distance free molecular dynamics. J. Mol. Biol. 246, 209-226.
-
(1995)
J. Mol. Biol.
, vol.246
, pp. 209-226
-
-
Cognet, J.A.H.1
Boulard, Y.2
Fazakerley, G.V.3
-
22
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Kenneth, M., Merz, J., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (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
Kenneth, M.5
Merz, J.6
Ferguson, D.M.7
Spellmeyer, D.C.8
Fox, T.9
Caldwell, J.W.10
Kollman, P.A.11
-
23
-
-
33846823909
-
Particle mesh Ewald-an N.Log9n method for Ewald sums in large systems
-
Darden, T., York, D. & Pedersen, L. (1993). Particle mesh Ewald-an N.log9n) method 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
-
24
-
-
0019387686
-
Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure
-
Dickerson, R. E. & Drew, H. R. (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
-
25
-
-
0027948889
-
The tyranny of the lattice
-
Dickerson, R. E., Goodsell, D. S. & Neidle, S. (1994). The tyranny of the lattice. Proc. Natl Acad. Sci. USA, 91, 3579-3583.
-
(1994)
Proc. Natl Acad. Sci. USA
, vol.91
, pp. 3579-3583
-
-
Dickerson, R.E.1
Goodsell, D.S.2
Neidle, S.3
-
26
-
-
0019843568
-
Structure of a B-DNA dodecamer. III. Geometry of hydration
-
Drew, H. R. & 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
-
27
-
-
0019558179
-
Structure of a B-DNA dodecamer: Conformation and dynamics
-
Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl Acad. Sci. USA, 78, 2179-2183.
-
(1981)
Proc. Natl Acad. Sci. USA
, vol.78
, pp. 2179-2183
-
-
Drew, H.R.1
Wing, R.M.2
Takano, T.3
Broka, C.4
Tanaka, S.5
Itakura, K.6
Dickerson, R.E.7
-
28
-
-
0020157572
-
Structure of a B-DNA dodecamer at 16 K
-
Drew, H. R., Samson, S. & Dickerson, R. E. (1982). Structure of a B-DNA dodecamer at 16 K. Proc. Natl Acad. Sci. USA, 79, 4040-4044.
-
(1982)
Proc. Natl Acad. Sci. USA
, vol.79
, pp. 4040-4044
-
-
Drew, H.R.1
Samson, S.2
Dickerson, R.E.3
-
29
-
-
84986437295
-
Gradient shake: An imporoved method for constrained energy minimization in macromolecular simulations
-
Duan, Y., Kumar, S., Rosenberg, J. M. & Kollman, P. (1995). Gradient shake: an imporoved method for constrained energy minimization in macromolecular simulations. J. Comput. Chem. 16, 1351-1356.
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1351-1356
-
-
Duan, Y.1
Kumar, S.2
Rosenberg, J.M.3
Kollman, P.4
-
30
-
-
0000877546
-
Sequence dependent hydration of DNA: Theoretical results
-
Elcock, A. H. & McCammon, J. A. (1995). Sequence dependent hydration of DNA: theoretical results. J. Am. Chem. Soc. 117, 10161-10162.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 10161-10162
-
-
Elcock, A.H.1
McCammon, J.A.2
-
31
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T. A., Lee, H. & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.A.4
Lee, H.5
Pedersen, L.G.6
-
32
-
-
0018793861
-
Temperature-dependent X-ray diffraction as a probe of protein structural dynamics
-
Frauenfelder, H., Petsko, G. A. & Tsernoglou, D. (1979). Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature, 280, 558-563.
-
(1979)
Nature
, vol.280
, pp. 558-563
-
-
Frauenfelder, H.1
Petsko, G.A.2
Tsernoglou, D.3
-
33
-
-
0028212564
-
Structural and dynamic characterization of the heterodimeric and homodimeric complexes of distamycin and 1-methylimidazole-2-carboxamide-netropsin bound to the minor groove of DNA
-
Geuerstanger, B. H., Jacobsen, J. P., Mrksich, M., Dervan, P. B. & Wemmer, D. E. (1994). Structural and dynamic characterization of the heterodimeric and homodimeric complexes of distamycin and 1-methylimidazole-2-carboxamide-netropsin bound to the minor groove of DNA. Biochemistry, 33, 3055-3062.
-
(1994)
Biochemistry
, vol.33
, pp. 3055-3062
-
-
Geuerstanger, B.H.1
Jacobsen, J.P.2
Mrksich, M.3
Dervan, P.B.4
Wemmer, D.E.5
-
34
-
-
0029092698
-
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations
-
Hunenberger, P. H., Mark, A. E. & van Gunsteren, W. F. (1995). Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. J. Mol. Biol. 252, 492-503.
-
(1995)
J. Mol. Biol.
, vol.252
, pp. 492-503
-
-
Hunenberger, P.H.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
35
-
-
0024276807
-
Anisotropy and anharmonicity of atomic flucturations in proteins: Implications for X-ray analysis
-
Ichiye, T. & Karplus, M. (1988). Anisotropy and anharmonicity of atomic flucturations in proteins: implications for X-ray analysis. Biochemistry, 27, 3487-3497.
-
(1988)
Biochemistry
, vol.27
, pp. 3487-3497
-
-
Ichiye, T.1
Karplus, M.2
-
36
-
-
0026717834
-
Normal mode refinement: Crystallographic refinement of protein dynamic structure. II. Application to human lysozyme
-
Kidera, A., Inaka, K., Matsushima, M. & Go, N. (1992). Normal mode refinement: crystallographic refinement of protein dynamic structure. II. Application to human lysozyme. J. Mol. Biol. 225, 477-486.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 477-486
-
-
Kidera, A.1
Inaka, K.2
Matsushima, M.3
Go, N.4
-
37
-
-
0025187081
-
Refinement of EcoRI endonuclease crystal structure: A revised protein chain tracing
-
Kim, Y. C., Grable, J. C., Love, R., Greene, P. J. & Rosenberg, J. M. (1990). Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science, 249, 1307-1309.
-
(1990)
Science
, vol.249
, pp. 1307-1309
-
-
Kim, Y.C.1
Grable, J.C.2
Love, R.3
Greene, P.J.4
Rosenberg, J.M.5
-
38
-
-
0000272892
-
Studies on the canonical DNA-EcoRI endonuclease complex and the EcoRI kink
-
(Sarma, R. H. & Sarma, M. H., eds), Adenine Press, New York
-
Kim, Y., Choi, J., Grable, J. C., Greene, P., Hager, P. & Rosenberg, J. M. (1994). Studies on the canonical DNA-EcoRI endonuclease complex and the EcoRI kink. In Structural Biology: The State of the Art (Sarma, R. H. & Sarma, M. H., eds), pp. 225-246, Adenine Press, New York.
-
(1994)
Structural Biology: The State of the Art
, pp. 225-246
-
-
Kim, Y.1
Choi, J.2
Grable, J.C.3
Greene, P.4
Hager, P.5
Rosenberg, J.M.6
-
39
-
-
0020692923
-
Ordered water structure around a B-DNA dodecamer. A quantitative study
-
Kopka, M. L., Fratini, A. V., Drew, H. R. & 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
-
40
-
-
0028578644
-
Molecular-dynamics simulations suggest that the EcoRI kink is an example of molecular strain
-
Kumar, S., Duan, Y., Kollman, P. A. & Rosenberg, J. M. (1994). Molecular-dynamics simulations suggest that the EcoRI kink is an example of molecular strain. J. Biomol. Struct. Dynam. 12, 487-525.
-
(1994)
J. Biomol. Struct. Dynam.
, vol.12
, pp. 487-525
-
-
Kumar, S.1
Duan, Y.2
Kollman, P.A.3
Rosenberg, J.M.4
-
41
-
-
0025904209
-
Rigid protein motion as a model for crystallographic temperature factors
-
Kuriyan, J. & Weis, W. L. (1991). Rigid protein motion as a model for crystallographic temperature factors. Proc. Natl Acad. Sci. USA, 88, 2773-2777.
-
(1991)
Proc. Natl Acad. Sci. USA
, vol.88
, pp. 2773-2777
-
-
Kuriyan, J.1
Weis, W.L.2
-
42
-
-
0023053635
-
Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics
-
Kuriyan, J., Petsko, G. A., Levy, R. M. & Karplus, M. (1986). Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. J. Mol. Biol. 190, 227-254.
-
(1986)
J. Mol. Biol.
, vol.190
, pp. 227-254
-
-
Kuriyan, J.1
Petsko, G.A.2
Levy, R.M.3
Karplus, M.4
-
43
-
-
0024058085
-
The definition of generalized helicoidal parameters and of axis curvature for irregular nuleic acids
-
Lavery, R. & Sklenar, H. (1988). The definition of generalized helicoidal parameters and of axis curvature for irregular nuleic acids. J. Biomol. Struct. Dynam. 6, 63-91.
-
(1988)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, H.2
-
44
-
-
0024539180
-
Defining the structure of irregular nucleic acids: Conventions and principles
-
Lavery, R. & Sklenar, H. (1989). Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dynam. 4, 655-667.
-
(1989)
J. Biomol. Struct. Dynam.
, vol.4
, pp. 655-667
-
-
Lavery, R.1
Sklenar, H.2
-
45
-
-
0001680774
-
A quantitative description of the conformation of biological macromolecules
-
(Sarma, R. H. & Sarma, M. H., eds), Adenine Press, New York
-
Lavery, R. & Sklenar, H. (1990). A quantitative description of the conformation of biological macromolecules. In Structure and Methods: DNA-Protein Complexes and Proteins (Sarma, R. H. & Sarma, M. H., eds), pp. 215-235, Adenine Press, New York.
-
(1990)
Structure and Methods: DNA-Protein Complexes and Proteins
, pp. 215-235
-
-
Lavery, R.1
Sklenar, H.2
-
46
-
-
0020262664
-
Computer simulation of DNA double-helix dynamics
-
Levitt, M. (1982). Computer simulation of DNA double-helix dynamics. Cold Spring Harbor Symp. Quant. Biol 47, 251-262.
-
(1982)
Cold Spring Harbor Symp. Quant. Biol
, vol.47
, pp. 251-262
-
-
Levitt, M.1
-
48
-
-
0024795316
-
The effects of truncating long-range forces on protein dynamics
-
Loncharich, R. J. & Brooks, B. R. (1989). The effects of truncating long-range forces on protein dynamics. Proteins: Struct. Funct. Genet. 6, 32-45.
-
(1989)
Proteins: Struct. Funct. Genet.
, vol.6
, pp. 32-45
-
-
Loncharich, R.J.1
Brooks, B.R.2
-
49
-
-
0030005364
-
Calculations of nucleic acid conformations
-
Louise-May, S., Auffinger, P. & Westhof, E. (1996). Calculations of nucleic acid conformations. Curr. Opin. Struct. Biol. 6, 289-298.
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 289-298
-
-
Louise-May, S.1
Auffinger, P.2
Westhof, E.3
-
50
-
-
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. Quart. Rev. Biophys. 11, 179-246.
-
(1978)
Quart. Rev. Biophys.
, vol.11
, pp. 179-246
-
-
Manning, G.S.1
-
52
-
-
0022964809
-
Structure of the DNA-EcoRI endonuclease recognition complex at 3 Å resolution
-
McClarin, J. A., Frederick, C. A., Wang, B. C., Greene, P., Boyer, H. W., Grable, J. & Rosenberg, J. M. (1986). Structure of the DNA-EcoRI endonuclease recognition complex at 3 Å resolution. Science, 234, 1526-1541.
-
(1986)
Science
, vol.234
, pp. 1526-1541
-
-
McClarin, J.A.1
Frederick, C.A.2
Wang, B.C.3
Greene, P.4
Boyer, H.W.5
Grable, J.6
Rosenberg, J.M.7
-
53
-
-
0000927175
-
Nanosecond molecular-dynamics simulations on the d(CGCGAATTCGCG) double helix in water
-
McConnell, K. J., Nirmala, R., Young, M. A., Ravishanker, G. & Beveridge, D. L. (1994a). Nanosecond molecular-dynamics simulations on the d(CGCGAATTCGCG) double helix in water. Biophys. J. 66, 391.
-
(1994)
Biophys. J.
, vol.66
, pp. 391
-
-
McConnell, K.J.1
Nirmala, R.2
Young, M.A.3
Ravishanker, G.4
Beveridge, D.L.5
-
54
-
-
0028052906
-
A nanosecond molecular-dynamics trajectory for a B-DNA double helix-evidence for substates
-
McConnell, K. J., Nirmala, R., Young, M. A., Ravishanker, G. & Beveridge, D. L. (1994b). 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.J.1
Nirmala, R.2
Young, M.A.3
Ravishanker, G.4
Beveridge, D.L.5
-
55
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
-
Miyamoto, S. & Kollman, P. A. (1992). SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13, 952-962.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
56
-
-
0019323773
-
Highly structured water network in crystals of a deoxydinucleoside-drug complex
-
Neidle, S., Berman, H. M. & Shieh, H. S. (1980). Highly structured water network in crystals of a deoxydinucleoside-drug complex. Nature, 288, 129-133.
-
(1980)
Nature
, vol.288
, pp. 129-133
-
-
Neidle, S.1
Berman, H.M.2
Shieh, H.S.3
-
57
-
-
0004279414
-
-
University of California, San Francisco
-
Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E. I., Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K. & Kollman, P. A. (1995). AMBER 4.1. University of California, San Francisco.
-
(1995)
AMBER 4.1
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.I.5
Ferguson, D.M.6
Seibel, G.L.7
Singh, U.C.8
Weiner, P.K.9
Kollman, P.A.10
-
58
-
-
0001015292
-
Structural characterization of a 2:1 distamycin A·d(CGCA-AATTGGC) complex by two-dimensional NMR
-
Pelton, J. G. & Wemmer, D. E. (1989). Structural characterization of a 2:1 distamycin A·d(CGCA-AATTGGC) complex by two-dimensional NMR. Proc. Natl Acad. Sci. USA, 86, 5723-5727.
-
(1989)
Proc. Natl Acad. Sci. USA
, vol.86
, pp. 5723-5727
-
-
Pelton, J.G.1
Wemmer, D.E.2
-
60
-
-
0023628497
-
Helix geometry, hydration, and G.A mismatch in a B-DNA decamer
-
Prive, G. G., Heinemann, U., Chandrasegaran, S., Kan, L. S., Kopka, M. L. & Dickerson, R. E. (1987). Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. Science, 238, 498-504.
-
(1987)
Science
, vol.238
, pp. 498-504
-
-
Prive, G.G.1
Heinemann, U.2
Chandrasegaran, S.3
Kan, L.S.4
Kopka, M.L.5
Dickerson, R.E.6
-
61
-
-
0024556774
-
Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows
-
Ravishanker, G., Swaminathan, S., Beveridge, D. L., Lavery, R. & Sklenar, H. (1989). Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows. J. Biomol. Struct. Dynam. 6, 669-699.
-
(1989)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 669-699
-
-
Ravishanker, G.1
Swaminathan, S.2
Beveridge, D.L.3
Lavery, R.4
Sklenar, H.5
-
62
-
-
0001076529
-
Structure and function f restriction endonucleases
-
191
-
Rosenberg, J. M. (191). Structure and function f restriction endonucleases. Curr. Opin. Struct. Biol. 1, 104-113.
-
Curr. Opin. Struct. Biol.
, vol.1
, pp. 104-113
-
-
Rosenberg, J.M.1
-
63
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Rychaert, J.-P., Ciccotti, G. & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Rychaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
65
-
-
0027138869
-
A systematic method for studying the spatial distribution of water molecules around nucleic acid bases
-
Schneider, B., Cohen, D. M., Schleifer, L., Srinivasan, A. R., Olson, W. K. & Berman, H. M. (1993). A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophy. J. 65, 2291-2303.
-
(1993)
Biophy. 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
-
66
-
-
84986534166
-
New sphericalcutoff methods for long-range forces in macromolecular simulation
-
Steinbach, P. J. & Brooks, B. R. (1994). New sphericalcutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem. 15, 667-683.
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 667-683
-
-
Steinbach, P.J.1
Brooks, B.R.2
-
67
-
-
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. & Beveridge, D. L. (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. Dynam. 6, 1093-1122.
-
(1989)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 1093-1122
-
-
Subramanian, P.S.1
Beveridge, D.L.2
-
68
-
-
0011212217
-
A Monte-Carlo simulation study of the aqueous hydration of d(CGCGCG) in Z-form
-
Subramanian, P. S. & Beveridge, D. L. (1993). A Monte-Carlo simulation study of the aqueous hydration of d(CGCGCG) in Z-form. Theor. Chim. Acta, 85, 3-15.
-
(1993)
Theor. Chim. Acta
, vol.85
, pp. 3-15
-
-
Subramanian, P.S.1
Beveridge, D.L.2
-
69
-
-
0024121512
-
Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG)*d(GCGCTTAAGCGC): Monte Carlo computer simulation
-
Subramanian, P. S., Ravishanker, G. & Beveridge, D. L. (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
-
70
-
-
0025338247
-
Theoretical account of the spine of hydration in the minor groove of duplex d(CGCGAATTCGCG)
-
Subramanian, P. S., Swaminathan, S. & Beveridge, D. L. (1990). Theoretical account of the spine of hydration in the minor groove of duplex d(CGCGAATTCGCG). J. Biomol. Struct. Dynam. 7, 1161-1165.
-
(1990)
J. Biomol. Struct. Dynam.
, vol.7
, pp. 1161-1165
-
-
Subramanian, P.S.1
Swaminathan, S.2
Beveridge, D.L.3
-
71
-
-
0025184515
-
Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI
-
Swaminathan, S., Ravishanker, G., Beveridge, D. L., Lavery, R., Etchebest, C. & Sklenar, H. (1990). Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI. Proteins: Struct. Funct. Genet. 8, 179-193.
-
(1990)
Proteins: Struct. Funct. Genet.
, vol.8
, pp. 179-193
-
-
Swaminathan, S.1
Ravishanker, G.2
Beveridge, D.L.3
Lavery, R.4
Etchebest, C.5
Sklenar, H.6
-
72
-
-
0004084360
-
Light scattering spectroscopy studies of the water molecules in DNA
-
(Westhof, E., ed.), The Macmillan Press Ltd, London
-
Tao, N. J. (1993). Light scattering spectroscopy studies of the water molecules in DNA. In Water and Biological Macromolecules (Westhof, E., ed.), pp. 266-292, The Macmillan Press Ltd, London.
-
(1993)
Water and Biological Macromolecules
, pp. 266-292
-
-
Tao, N.J.1
-
73
-
-
22944467757
-
Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
-
Verlet, L. (1967). Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159, 98-103.
-
(1967)
Phys. Rev.
, vol.159
, pp. 98-103
-
-
Verlet, L.1
-
74
-
-
0029139897
-
Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution
-
Weerasinghe, S., Smith, P. E., Mohan, V., Cheng, Y.-K. & Pettitt, B. M. (1995). Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution. J. Am. Chem. Soc. 117, 2147-2158.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 2147-2158
-
-
Weerasinghe, S.1
Smith, P.E.2
Mohan, V.3
Cheng, Y.-K.4
Pettitt, B.M.5
-
75
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., Jr & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta S., Jr.7
Weiner, P.8
-
76
-
-
84988053694
-
An all atom force field for simulation of proteins and nucleic acids
-
Weiner, S. J., Kollman, P. A., Nguyen, D. T. & Cse, D. A. (1986). An all atom force field for simulation of proteins and nucleic acids. J. Comp. Chem. 7, 230-252.
-
(1986)
J. Comp. Chem.
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Cse, D.A.4
-
77
-
-
0000514393
-
Structural water bridges in nucleic acids
-
193 (Westhof, E., ed.), The Macmillan Press Ltd, London
-
Westhof, E. (193). Structural water bridges in nucleic acids. In Water and Biological Macromolecules (Westhof, E., ed.), pp. 226-243, The Macmillan Press Ltd, London.
-
Water and Biological Macromolecules
, pp. 226-243
-
-
Westhof, E.1
-
78
-
-
0019331504
-
Crystal structure analysis of a complete turn of B-DNA
-
Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1980). Crystal structure analysis of a complete turn of B-DNA. Nature, 287, 755-758.
-
(1980)
Nature
, vol.287
, pp. 755-758
-
-
Wing, R.1
Drew, H.2
Takano, T.3
Broka, C.4
Tanaka, S.5
Itakura, K.6
Dickerson, R.E.7
-
79
-
-
0026511587
-
Toward a dynamical structure of DNA: Comparison of theoretical and experimental NOE intensities
-
Withka, J. M., Swaminathan, S., Srinivasan, J., Beveridge, D. L. & Bolton, P. H. (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
-
80
-
-
33748674257
-
B to A transition of DNA on the nanosecond time scale
-
Yang, L. & Pettitt, B. M. (1996). B to A transition of DNA on the nanosecond time scale. J. Phys. Chem. 100, 2564-2566.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 2564-2566
-
-
Yang, L.1
Pettitt, B.M.2
-
81
-
-
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., Darden, T. A. & Pedersen, L. G. (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
-
82
-
-
0029110156
-
Toward the accurate modeling of DNA: The importance of long-range electrostatics
-
York, D. M., Yang, W., Lee, H., Darden, T. & Pedersen, L. G. (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
-
83
-
-
0029109915
-
Molecular dynamics of RNA with the OPLS force field. Aqueous simulation of a hairpin containing a tetranucleotide loop
-
Zichi, D. A. (1995). Molecular dynamics of RNA with the OPLS force field. Aqueous simulation of a hairpin containing a tetranucleotide loop. J. Am. Chem. Soc. 117, 2957-2969.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 2957-2969
-
-
Zichi, D.A.1
|