-
1
-
-
0021380354
-
Multistep Brownian dynamics: Application to short wormlike chain
-
Allison, S. A., and J. A. McCammon. 1984. Multistep Brownian dynamics: application to short wormlike chain. Biopolymers. 23:363-375.
-
(1984)
Biopolymers
, vol.23
, pp. 363-375
-
-
Allison, S.A.1
McCammon, J.A.2
-
2
-
-
36749121933
-
Theory of twisting and bending of chain macromolecules: Analysis of the fluorescence depolarization of DNA
-
Barkley, M. D., and B. Zimm. 1979. Theory of twisting and bending of chain macromolecules: analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70:2991-3007.
-
(1979)
J. Chem. Phys.
, vol.70
, pp. 2991-3007
-
-
Barkley, M.D.1
Zimm, B.2
-
3
-
-
0028064296
-
Canonical analysis of correlated atomic motions in DNA from molecular dynamics simulation
-
Briki, F., and D. Genest. 1994. Canonical analysis of correlated atomic motions in DNA from molecular dynamics simulation. Biophys. Chem. 52:35-43.
-
(1994)
Biophys. Chem.
, vol.52
, pp. 35-43
-
-
Briki, F.1
Genest, D.2
-
4
-
-
0029026380
-
Rigid body motions of sub-units in DNA: A correlation analysis of a 200 ps molecular dynamics simulation
-
Briki, F., and D. Genest. 1995. Rigid body motions of sub-units in DNA: a correlation analysis of a 200 ps molecular dynamics simulation. J. Biomol. Struct. Dyn. 12:1063-1082.
-
(1995)
J. Biomol. Struct. Dyn.
, vol.12
, pp. 1063-1082
-
-
Briki, F.1
Genest, D.2
-
5
-
-
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 T.E. III1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
6
-
-
0028184699
-
Kinetics of DNA supercoiling studied by Brownian dynamics simulation
-
Chirico, G., and J. Langowski. 1994. Kinetics of DNA supercoiling studied by Brownian dynamics simulation. Biopolymers. 34:415-433.
-
(1994)
Biopolymers
, vol.34
, pp. 415-433
-
-
Chirico, G.1
Langowski, J.2
-
7
-
-
0030064676
-
DNA: An extensible molecule
-
Cluzel, P., A. Lebrun, C. Heller, R. Lavery, J. L. Viovy, D. Chatenay, and F. Caron. 1996. DNA: an extensible molecule. Science. 271:792-794.
-
(1996)
Science
, vol.271
, pp. 792-794
-
-
Cluzel, P.1
Lebrun, A.2
Heller, C.3
Lavery, R.4
Viovy, J.L.5
Chatenay, D.6
Caron, F.7
-
8
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids and organic molecules
-
Cornell, W. D., P. Cieplak, C. I. Bayley, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmayer, 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
Bayley, C.I.3
Gould, I.R.4
Merz K.M., Jr.5
Ferguson, D.M.6
Spellmayer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
9
-
-
33846823909
-
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
-
Darden, T. A., D. M. York, and L. G. Pedersen. 1993. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.A.1
York, D.M.2
Pedersen, L.G.3
-
10
-
-
0024974308
-
Definitions and nomenclature of nucleic acid structure parameters
-
Dickerson, R. E., M. Bansal, C. R. Calladine, S. Diekmann, W. N. Hunter, O. Kennard, R. Lavery, H. C. M. Nelson, W. K. Olson, W. Saenger, Z. Shakked, H. Sklenar, D. M. Soumpasis, C. S. Tung, E. von Kitzi, A. H. J. Wang, and V. B. Zhurkin. 1989. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol 205:787-791.
-
(1989)
J. Mol. Biol
, vol.205
, pp. 787-791
-
-
Dickerson, R.E.1
Bansal, M.2
Calladine, C.R.3
Diekmann, S.4
Hunter, W.N.5
Kennard, O.6
Lavery, R.7
Nelson, H.C.M.8
Olson, W.K.9
Saenger, W.10
Shakked, Z.11
Sklenar, H.12
Soumpasis, D.M.13
Tung, C.S.14
Von Kitzi, E.15
Wang, A.H.J.16
Zhurkin, V.B.17
-
11
-
-
0031808069
-
Structural equilibrium of DNA represented with different force fields
-
Feig, M., and B. M. Pettitt. 1998. Structural equilibrium of DNA represented with different force fields. Biophys. J. 75:134-149.
-
(1998)
Biophys. J.
, vol.75
, pp. 134-149
-
-
Feig, M.1
Pettitt, B.M.2
-
12
-
-
0031836876
-
Sequence-dependent dynamics of TATA-box binding sites
-
Flatters, D., and R. Lavery. 1998. Sequence-dependent dynamics of TATA-box binding sites. Biophys. J. 75:372-381.
-
(1998)
Biophys. J.
, vol.75
, pp. 372-381
-
-
Flatters, D.1
Lavery, R.2
-
13
-
-
0030958316
-
Conformational properties of the TATA-box binding sequence of DNA
-
Flatters, D., M. A. Young, D. L. Beveridge, and R. Lavery. 1997. Conformational properties of the TATA-box binding sequence of DNA. J. Biomol. Struct. Dyn. 14:757-765.
-
(1997)
J. Biomol. Struct. Dyn.
, vol.14
, pp. 757-765
-
-
Flatters, D.1
Young, M.A.2
Beveridge, D.L.3
Lavery, R.4
-
14
-
-
0009737677
-
Collective-variable Monte Carlo simulation of DNA
-
Gabb, H. A., C. Prevost, G. Bertucat, C. H. Robert, and R. Lavery. 1997. Collective-variable Monte Carlo simulation of DNA. J. Comp. Chem. 18:2001-2011.
-
(1997)
J. Comp. Chem.
, vol.18
, pp. 2001-2011
-
-
Gabb, H.A.1
Prevost, C.2
Bertucat, G.3
Robert, C.H.4
Lavery, R.5
-
15
-
-
0030729494
-
Search for rigid subdomains in DNA from molecular dynamics simulations
-
Gaudin, F., G. Lancelot, and D. Genest. 1997. Search for rigid subdomains in DNA from molecular dynamics simulations. J. Biomol. Struct. Dyn. 15:357-367.
-
(1997)
J. Biomol. Struct. Dyn.
, vol.15
, pp. 357-367
-
-
Gaudin, F.1
Lancelot, G.2
Genest, D.3
-
16
-
-
0030038364
-
How long does DNA keep the memory of its conformation? A time-dependent canonical correlation analysis of molecular dynamics simulation
-
Genest, D. 1996. How long does DNA keep the memory of its conformation? A time-dependent canonical correlation analysis of molecular dynamics simulation. Biopolymers. 38:389-399.
-
(1996)
Biopolymers
, vol.38
, pp. 389-399
-
-
Genest, D.1
-
17
-
-
0031896634
-
Motion of groups of atoms in DNA studied by molecular dynamics simulation
-
Genest, D. 1998. Motion of groups of atoms in DNA studied by molecular dynamics simulation. Eur. Biophys. J. 27:283-289.
-
(1998)
Eur. Biophys. J.
, vol.27
, pp. 283-289
-
-
Genest, D.1
-
18
-
-
0018274576
-
Fluorescence anisotropy decay due to rotational Brownian motion of ethidium intercalated in double strand DNA
-
Genest, D., and P. Wahl. 1978. Fluorescence anisotropy decay due to rotational Brownian motion of ethidium intercalated in double strand DNA. Biochim. Biophys. Acta. 52:502-509.
-
(1978)
Biochim. Biophys. Acta
, vol.52
, pp. 502-509
-
-
Genest, D.1
Wahl, P.2
-
19
-
-
0000793351
-
On the sampling theory of roots of determinantal equations
-
Girshick, M. A. 1939. On the sampling theory of roots of determinantal equations. Ann. Math. Stat. 10:203-224.
-
(1939)
Ann. Math. Stat.
, vol.10
, pp. 203-224
-
-
Girshick, M.A.1
-
20
-
-
0023256126
-
A single mode of base pair opening drives imino proton exchange
-
Guéron, M., M. Kochoyan, and J. L. Leroy. 1987. A single mode of base pair opening drives imino proton exchange. Nature. 328:89-92.
-
(1987)
Nature
, vol.328
, pp. 89-92
-
-
Guéron, M.1
Kochoyan, M.2
Leroy, J.L.3
-
21
-
-
0032577387
-
X-ray diffuse scattering and rigid-body motions in crystalline lysozyme probed by molecular dynamics simulation
-
Hery, S., D. Genest, and J. C. Smith. 1998. X-ray diffuse scattering and rigid-body motions in crystalline lysozyme probed by molecular dynamics simulation. J. Mol. Biol. 279:303-319.
-
(1998)
J. Mol. Biol.
, vol.279
, pp. 303-319
-
-
Hery, S.1
Genest, D.2
Smith, J.C.3
-
22
-
-
0019330812
-
Internal motions in deoxyribonucleic acid II
-
Hogan, M. E., and O. Jardetzsky. 1980. Internal motions in deoxyribonucleic acid II. Biochemistry. 19:3460-3468.
-
(1980)
Biochemistry
, vol.19
, pp. 3460-3468
-
-
Hogan, M.E.1
Jardetzsky, O.2
-
23
-
-
0032573605
-
Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition
-
Jian, H., T. Schlick, and A. Vologodskii. 1998. Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition. J. Mol. Biol. 284:287-296.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 287-296
-
-
Jian, H.1
Schlick, T.2
Vologodskii, A.3
-
24
-
-
0027504913
-
Crystal structure of a yeast TBP/TATA-box complex
-
Kim, Y., J. H. Gieger, S. Hahn, and P. B. Sigler. 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature. 365:512-520.
-
(1993)
Nature
, vol.365
, pp. 512-520
-
-
Kim, Y.1
Gieger, J.H.2
Hahn, S.3
Sigler, P.B.4
-
25
-
-
0031880233
-
A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes
-
Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys. J. 74:780-788.
-
(1998)
Biophys. J.
, vol.74
, pp. 780-788
-
-
Klenin, K.1
Merlitz, H.2
Langowski, J.3
-
27
-
-
0002993546
-
Modeling nucleic acids: Fine structure, flexibility and conformational transitions
-
Lavery, R. 1994. Modeling nucleic acids: fine structure, flexibility and conformational transitions. Adv. Comput. Biol. 1:69-145.
-
(1994)
Adv. Comput. Biol.
, vol.1
, pp. 69-145
-
-
Lavery, R.1
-
28
-
-
0021831321
-
Proton exchange and base pair opening of poly(rA)·poly(rU) and poly(rI)·poly(rC)
-
Leroy, J. L., D. Broseta, and M. Guéron. 1985. Proton exchange and base pair opening of poly(rA)·poly(rU) and poly(rI)·poly(rC). J. Mol. Biol. 184:165-168.
-
(1985)
J. Mol. Biol.
, vol.184
, pp. 165-168
-
-
Leroy, J.L.1
Broseta, D.2
Guéron, M.3
-
29
-
-
0018350099
-
Gene duplication in the structural evolution of chymotrypsin
-
McLachlan, A. D. 1979. Gene duplication in the structural evolution of chymotrypsin. J. Mol. Biol. 128:49-79.
-
(1979)
J. Mol. Biol.
, vol.128
, pp. 49-79
-
-
McLachlan, A.D.1
-
30
-
-
0023781527
-
Modification of DNA dynamics by platinum drug binding: A time-dependent fluorescence depolarization study of the interaction of cis- and trans-diamminedichloroplatinum(II) with DNA
-
Millard, D. P., K. M. Ho, and M. J. Aroney. 1988. Modification of DNA dynamics by platinum drug binding: a time-dependent fluorescence depolarization study of the interaction of cis- and trans-diamminedichloroplatinum(II) with DNA. Biochemistry. 27:8599-8606.
-
(1988)
Biochemistry
, vol.27
, pp. 8599-8606
-
-
Millard, D.P.1
Ho, K.M.2
Aroney, M.J.3
-
31
-
-
0030005131
-
Simulating DNA at low resolution
-
Olson, W. K. 1996. Simulating DNA at low resolution. Curr. Opin. Struct. Biol. 6:242-256.
-
(1996)
Curr. Opin. Struct. Biol.
, vol.6
, pp. 242-256
-
-
Olson, W.K.1
-
32
-
-
0032540859
-
Sequence dependent DNA structure, the role of the sugar-phosphate backbone
-
Packer, M. J., and C. A. Hunter. 1998. Sequence dependent DNA structure, the role of the sugar-phosphate backbone. J. Mol. Biol. 280:407-420.
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 407-420
-
-
Packer, M.J.1
Hunter, C.A.2
-
33
-
-
0004279414
-
-
University of California at San Francisco, San Francisco, CA
-
Pearlman, D. A., D. A. Case, G. W. Caldwell, W. S. Ross, T. E. Cheatham, III, D. M. Ferguson, G. L. Seibel, U. C. Singh, P. Weiner, and P. A. Kollman, editors. 1995. AMBER 4.1. University of California at San Francisco, San Francisco, CA.
-
(1995)
AMBER 4.1
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, G.W.3
Ross, W.S.4
Cheatham T.E. III5
Ferguson, D.M.6
Seibel, G.L.7
Singh, U.C.8
Weiner, P.9
Kollman, P.A.10
-
34
-
-
33646940952
-
Numerical integration of Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., G. Cicotti, and H. J. C. Berendsen. 1977. Numerical integration of Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Physiol. 23: 327-341.
-
(1977)
J. Comp. Physiol.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Cicotti, G.2
Berendsen, H.J.C.3
-
35
-
-
0029066852
-
Modeling superhelical DNA: Recent analytical and dynamic approaches
-
Schlick, T. 1995. Modeling superhelical DNA: recent analytical and dynamic approaches. Curr. Opin. Struct. Biol. 5:145-262.
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 145-262
-
-
Schlick, T.1
-
36
-
-
0026554929
-
Supercoiled DNA energetics and dynamics by computer simulation
-
Schlick, T., and W. K. Olson. 1992. Supercoiled DNA energetics and dynamics by computer simulation. J. Mol. Biol. 223:1089-1119.
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 1089-1119
-
-
Schlick, T.1
Olson, W.K.2
-
37
-
-
0030024985
-
Overstretching DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith, S. B., Y. Cui, and C. Bustamante. 1996. Overstretching DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:795-799.
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.2
Bustamante, C.3
-
38
-
-
0000115258
-
Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/water mixture. Theoretical considerations of the A to and from B transition
-
Sprous, D., M. A. Young, and D. L. Beveridge. 1998. Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/water mixture. Theoretical considerations of the A to and from B transition. J. Phys. Chem. 102:4658-4667.
-
(1998)
J. Phys. Chem.
, vol.102
, pp. 4658-4667
-
-
Sprous, D.1
Young, M.A.2
Beveridge, D.L.3
-
39
-
-
0024590138
-
Molecular mechanics model of supercoiled DNA
-
Tan, R. K., and S. C. Harvey. 1989. Molecular mechanics model of supercoiled DNA. J. Mol. Biol. 205:573-591.
-
(1989)
J. Mol. Biol.
, vol.205
, pp. 573-591
-
-
Tan, R.K.1
Harvey, S.C.2
-
40
-
-
0019077298
-
Torsion dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral θ29 DNA
-
Thomas, J. C., S. A. Allison, C. L. Appelof, and M. Schurr. 1980. Torsion dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral θ29 DNA. Biophys. Chem. 12:177-188.
-
(1980)
Biophys. Chem.
, vol.12
, pp. 177-188
-
-
Thomas, J.C.1
Allison, S.A.2
Appelof, C.L.3
Schurr, M.4
-
41
-
-
84947395538
-
-
Biomolecular Software, University of Groningen, Groningen, the Netherlands
-
van Gunsteren, W. F., and H. J. C. Berendsen. 1986. GROMOS 87 package, Biomos. Biomolecular Software, University of Groningen, Groningen, the Netherlands.
-
(1986)
GROMOS 87 Package, Biomos
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
42
-
-
0014734013
-
Decay of fluorescence emission anisotropy of the ethidium bromide-DNA complex. Evidence for an internal motion in DNA
-
Wahl, P., C. Paoletti, and J. B. Le Pecq. 1970. Decay of fluorescence emission anisotropy of the ethidium bromide-DNA complex. Evidence for an internal motion in DNA. Proc. Natl. Acad. Sci. USA. 65:417-421.
-
(1970)
Proc. Natl. Acad. Sci. USA
, vol.65
, pp. 417-421
-
-
Wahl, P.1
Paoletti, C.2
Le Pecq, J.B.3
-
43
-
-
0025800219
-
Static and statistical bending of DNA evaluated by Monte Carlo simulations
-
Zhurkin, V. B., N. B. Ulyanov, A. A. Gorin, and R. L. Jernigan. 1991. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc. Natl. Acad. Sci. USA. 88:7046-7050.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 7046-7050
-
-
Zhurkin, V.B.1
Ulyanov, N.B.2
Gorin, A.A.3
Jernigan, R.L.4
|