-
1
-
-
0032873823
-
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins
-
Ponomarenko M.P., Pomonomarenko J.V., Frolov A.S., Podkolodny N.L., Savinkova L.K., Kolchanov N.A., Overton G.C. 1999. Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins. Bioinformatics. 15, 687-695.
-
(1999)
Bioinformatics
, vol.15
, pp. 687-695
-
-
Ponomarenko, M.P.1
Pomonomarenko, J.V.2
Frolov, A.S.3
Podkolodny, N.L.4
Savinkova, L.K.5
Kolchanov, N.A.6
Overton, G.C.7
-
3
-
-
33747378396
-
-
Russian source
-
-
-
-
4
-
-
0019558179
-
Structure of B-DNA dodecamer: Conformation and dynamics
-
Drew H.R., Wing R.M., Takano T., Broka C., Tanaka S., Itikura K., Dickerson R.E. 1981. Structure of 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
Itikura, K.6
Dickerson, R.E.7
-
6
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson W.K., Gorin A.A., Lu X.-J., Hock L.M., Zhurkin V.B. 1998. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA. 95, 11163-11168.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.-J.3
Hock, L.M.4
Zhurkin, V.B.5
-
7
-
-
0028225644
-
The crystal structure of C-C-A-T-T-A-A-T-G-G: Implications for bending of B-DNA at T-A steps
-
Goodsell D.S., Kaczor-Grzeskowiak M., Dickerson R.E. 1994. The crystal structure of C-C-A-T-T-A-A-T-G-G: implications for bending of B-DNA at T-A steps. J. Mol. Biol. 239, 79-96.
-
(1994)
J. Mol. Biol.
, vol.239
, pp. 79-96
-
-
Goodsell, D.S.1
Kaczor-Grzeskowiak, M.2
Dickerson, R.E.3
-
8
-
-
0027318463
-
Sequence-dependent DNA structure: The role of base stacking interactions
-
Hunter C.A. 1993. Sequence-dependent DNA structure: the role of base stacking interactions. J. Mol. Biol. 230, 1025-1054.
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 1025-1054
-
-
Hunter, C.A.1
-
9
-
-
0030003963
-
Propeller twisting of base pairs and the conformational mobility of dinucleotide steps in DNA
-
El Hassan M.A., Calladine CR. 1996. Propeller twisting of base pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol. 259, 95-103.
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 95-103
-
-
El Hassan, M.A.1
Calladine, C.R.2
-
10
-
-
0032499635
-
The B-DNA dodecamer at high resolution reveals a spine of water on sodium
-
Shiu X., McFail-Isom L., Hu G.G., Williams L.D. 1998. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry. 37, 8341-8355.
-
(1998)
Biochemistry
, vol.37
, pp. 8341-8355
-
-
Shiu, X.1
McFail-Isom, L.2
Hu, G.G.3
Williams, L.D.4
-
11
-
-
0033594498
-
A hydrat-ion spine in a B-DNA minor grove
-
Tereshko V., Minasov G., Egli M. 1999. A hydrat-ion spine in a B-DNA minor grove. J. Am. Chem. Soc. 121, 3590-3595.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 3590-3595
-
-
Tereshko, V.1
Minasov, G.2
Egli, M.3
-
12
-
-
0033600794
-
Absence of monovalent cations in the the croslinked dodecamer CGCGAATTCGCG
-
Chiu T.K., Kaczor-Grzekowiak M., Dickerson R.E. 1999. Absence of monovalent cations in the the croslinked dodecamer CGCGAATTCGCG. J. Mol. Biol. 292, 589-608.
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 589-608
-
-
Chiu, T.K.1
Kaczor-Grzekowiak, M.2
Dickerson, R.E.3
-
14
-
-
0031423949
-
Crystal studies of B-DNA: The answers and the questions
-
Berman H.M. 1997. Crystal studies of B-DNA: the answers and the questions. Biopolymers. 44, 23-44.
-
(1997)
Biopolymers
, vol.44
, pp. 23-44
-
-
Berman, H.M.1
-
15
-
-
0029872258
-
A useful role for static models in elucidating the behaviour of DNA in solution
-
Calladine C.R., Drew H.R. 1996. A useful role for static models in elucidating the behaviour of DNA in solution. J. Mol. Biol. 257, 479-485.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 479-485
-
-
Calladine, C.R.1
Drew, H.R.2
-
16
-
-
0043203406
-
Crystal structures of A-DNA duplexes
-
Wahl M.C., Sundaralingam M. 1997. Crystal structures of A-DNA duplexes. Biopolmers. 44, 45-63.
-
(1997)
Biopolmers
, vol.44
, pp. 45-63
-
-
Wahl, M.C.1
Sundaralingam, M.2
-
17
-
-
0033585580
-
The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution
-
Tereshko V., Minasov G., Egli M. 1999. The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J. Am. Chem. Soc. 121, 470-471.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 470-471
-
-
Tereshko, V.1
Minasov, G.2
Egli, M.3
-
18
-
-
0032515407
-
Sterechemistry of binding of metal cations and water to a phosphate group
-
Schneider B., Kabelae M. 1998. Sterechemistry of binding of metal cations and water to a phosphate group. J. Am. Chem. Soc. 120, 161-165.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 161-165
-
-
Schneider, B.1
Kabelae, M.2
-
19
-
-
0031755274
-
Hydration of the phosphate groups in double-helix DNA
-
Schneider B., Patel K., Berman H.M. 1998. Hydration of the phosphate groups in double-helix DNA. Biophys. J. 75, 2422-2434.
-
(1998)
Biophys. J.
, vol.75
, pp. 2422-2434
-
-
Schneider, B.1
Patel, K.2
Berman, H.M.3
-
20
-
-
0034681195
-
Sequence specific binding of counter ions to B-DNA
-
Denisov V.P., Halle B. 2000. Sequence specific binding of counter ions to B-DNA. Proc. Natl. Acad. Sci. USA. 97, 629-633.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 629-633
-
-
Denisov, V.P.1
Halle, B.2
-
22
-
-
0028931709
-
B-DNA twisting correlated with pair morphology
-
Gorin A.A., Zhurkin V.B., Olson W.K. 1995. B-DNA twisting correlated with 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
-
23
-
-
0032168436
-
Rod models of DNA: Sequence-dependent anisotropic elastic modeling of local bending phenomena
-
Munteanu M.G., Vlahovicek K., Parthasarathy S., Simon I., Pongor S. 1998. Rod models of DNA: sequence-dependent anisotropic elastic modeling of local bending phenomena. TIBS. 23, 341-347.
-
(1998)
TIBS
, vol.23
, pp. 341-347
-
-
Munteanu, M.G.1
Vlahovicek, K.2
Parthasarathy, S.3
Simon, I.4
Pongor, S.5
-
24
-
-
0027961109
-
The influence of salt on the structure and energetics of supercoiled DNA
-
Schlick T., Olson W.K. 1994. The influence of salt on the structure and energetics of supercoiled DNA. Biophys. J. 67, 2146-2166.
-
(1994)
Biophys. J.
, vol.67
, pp. 2146-2166
-
-
Schlick, T.1
Olson, W.K.2
-
25
-
-
0028819366
-
Modulation of intramolecular interctions in superhelical DNA by curved sequences: A Monte Carlo study
-
Klenin K.V., Frank-Kamenetskii M.D., Langovski J. 1995. Modulation of intramolecular interctions in superhelical DNA by curved sequences: a Monte Carlo study. Biophys. J. 68, 81-88.
-
(1995)
Biophys. J.
, vol.68
, pp. 81-88
-
-
Klenin, K.V.1
Frank-Kamenetskii, M.D.2
Langovski, J.3
-
26
-
-
0026554929
-
Supercoiled DNA energetics and dynamics by computer simulation
-
Schlick T., Olson W.K. 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
-
27
-
-
0030005131
-
Simulating DNA at low resolution
-
Olson W. 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.1
-
28
-
-
0020262664
-
Computer simulation of DNA double helix dynamics
-
Levit M. 1983. Computer simulation of DNA double helix dynamics. Cold Spring Harbor Symp. Quant. Biol. 47, 251-262.
-
(1983)
Cold Spring Harbor Symp. Quant. Biol.
, vol.47
, pp. 251-262
-
-
Levit, M.1
-
29
-
-
0032054952
-
Simulations of the molecular dynamics of nucleic acid
-
Auffinger P., Westhof E. 1998. Simulations of the molecular dynamics of nucleic acid. Curr. Opin. Struct. Biol. 8, 227-236.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 227-236
-
-
Auffinger, P.1
Westhof, E.2
-
31
-
-
5744249209
-
Equation of state calculations by fast computing mashine
-
Metropolis N.A., Rosenbluth A.W., Rosenbluth N.M., Teller A.H., Teller E. 1953. Equation of state calculations by fast computing mashine. J. Chem. Phys. 21, 1087-1092.
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.A.1
Rosenbluth, A.W.2
Rosenbluth, N.M.3
Teller, A.H.4
Teller, E.5
-
33
-
-
0024066560
-
On the multiple-minima problem in the conformational analysis of polypeptides. An electrostatically driven Monte Carlo method
-
Ripoll D., Scheraga H.A. 1988. On the multiple-minima problem in the conformational analysis of polypeptides. An electrostatically driven Monte Carlo method. Biopolymers. 27, 1283-1303.
-
(1988)
Biopolymers
, vol.27
, pp. 1283-1303
-
-
Ripoll, D.1
Scheraga, H.A.2
-
34
-
-
0000666868
-
Smart walking: A new methods for Boltzman sampling of protein conformations
-
Zhou R., Berne B.J. 1997. Smart walking: a new methods for Boltzman sampling of protein conformations. J. Chem. Phys. 107, 9185-9196.
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 9185-9196
-
-
Zhou, R.1
Berne, B.J.2
-
35
-
-
0032561384
-
A glimpse of the holy grail?
-
Berendsen H.J.C. 1998. A glimpse of the holy grail? Science. 282, 642-643.
-
(1998)
Science
, vol.282
, pp. 642-643
-
-
Berendsen, H.J.C.1
-
36
-
-
0002625135
-
Molecular dynamics simulations: The limit and beyond
-
Eds. Deuflhard P., Hermans J. Berlin: Springer
-
Berendsen H.J.C. 1999. Molecular dynamics simulations: The limit and beyond. In Computational Molecular Dynamics: Challenges, Methods, Ideas. Eds. Deuflhard P., Hermans J. Berlin: Springer, 3-36.
-
(1999)
Computational Molecular Dynamics: Challenges, Methods, Ideas
, pp. 3-36
-
-
Berendsen, H.J.C.1
-
37
-
-
33747335525
-
-
URL: 2000. GROMOS96 Home page: http://www.igc.ethz.ch/gromos/; URL: 2002. CHARMM Home Page: http://www.scripps.edu/brooks/charmm_docs/; URL: SIGMA 2002. http://femto.med.unc.edu/SIGMA/index.html; URL: 2001. GROMACS home page, http://www.gromacs.org
-
URL: 2001. AMBER6 Home page: http://www.amber.ucsf.edu/amber/index.html; URL: 2000. GROMOS96 Home page: http://www.igc.ethz.ch/gromos/; URL: 2002. CHARMM Home Page: http://www.scripps.edu/brooks/charmm_docs/; URL: SIGMA 2002. http://femto.med.unc.edu/SIGMA/index.html; URL: 2001. GROMACS home page, http://www.gromacs.org/.
-
(2001)
-
-
-
38
-
-
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., Merz K.M., 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. Amer. Chem. Soc. 117, 5179-5197.
-
(1995)
J. Amer. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
39
-
-
84988053694
-
An all-atom force fieled for simulation of proteins and nucleic acids
-
Weiner S.J., Kollam P.A., Nguyen D.T., Case D.A. 1986. An all-atom force fieled for simulation of proteins and nucleic acids. J. Comp. Chem. 7, 230-249.
-
(1986)
J. Comp. Chem.
, vol.7
, pp. 230-249
-
-
Weiner, S.J.1
Kollam, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
40
-
-
84986512474
-
CHARMM: A program for macromolecular energy calculation, minimization and dynamics calculation
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. 1983. CHARMM: A program for macromolecular energy calculation, minimization and dynamics calculation. J. Comp. Chem. 4, 187-208.
-
(1983)
J. Comp. Chem.
, vol.4
, pp. 187-208
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
41
-
-
33845550595
-
Energy parameters in polypetides. Upgrating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occuring amino acids
-
Nemethy G., Pottle M.S., Scheraga H.A. 1983. Energy parameters in polypetides. Upgrating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occuring amino acids. J. Phys. Chem. 87, 1883-1901.
-
(1983)
J. Phys. Chem.
, vol.87
, pp. 1883-1901
-
-
Nemethy, G.1
Pottle, M.S.2
Scheraga, H.A.3
-
42
-
-
0001731773
-
Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
-
Nemethy G., Gibbson K.D., Palmer K.A., Yoon C.N., Paterlini G., Zagary A., Ramsey S., Scheraga H.A. 1992. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96, 6472-6489.
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 6472-6489
-
-
Nemethy, G.1
Gibbson, K.D.2
Palmer, K.A.3
Yoon, C.N.4
Paterlini, G.5
Zagary, A.6
Ramsey, S.7
Scheraga, H.A.8
-
43
-
-
33645941402
-
The OPLS potential functions for protein. Energy minimization for crystals of cyclic peptides and crambin
-
Jorgensen W.J., Tirado-Rives J. 1988. The OPLS potential functions for protein. Energy minimization for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110, 16570-1666.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 16570-21666
-
-
Jorgensen, W.J.1
Tirado-Rives, J.2
-
44
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen W.L., Maxwell D.S., Tirado-Rives J. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118, 11225-11239.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11239
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
45
-
-
0001751804
-
Parametrization of aliphatic Clin united atoms of GROMOS96 force field
-
Daura X., Mark A.E., van Gunsteren W.F. 1998. Parametrization of aliphatic Clin united atoms of GROMOS96 force field. J. Comp. Chem. 19, 535-547.
-
(1998)
J. Comp. Chem.
, vol.19
, pp. 535-547
-
-
Daura, X.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
46
-
-
0037571112
-
Merk molecular force field. 1. Basis, form, scope, parametrization and performance of MMFF94
-
Halgren T. A. 1996. Merk molecular force field. 1. Basis, form, scope, parametrization and performance of MMFF94. J. Comp. Chem. 17, 490-519.
-
(1996)
J. Comp. Chem.
, vol.17
, pp. 490-519
-
-
Halgren, T.A.1
-
47
-
-
0030021471
-
Bio-molecular dynamics comes to age
-
Berendsen H.J.C. 1996. Bio-molecular dynamics comes to age. Science. 271, 954-955.
-
(1996)
Science
, vol.271
, pp. 954-955
-
-
Berendsen, H.J.C.1
-
48
-
-
3042524904
-
RESP: The method to optimize atomic charges
-
Bayly C, Cieplak P., Cornell W., Kollman P.A. 1993. RESP: The method to optimize atomic charges. J. Phys. Chem. 97, 10269-10280.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.1
Cieplak, P.2
Cornell, W.3
Kollman, P.A.4
-
49
-
-
0000795938
-
Free energies of hydration and pure liquid properties of hydrocarbons from the OPLS all atom model
-
Kaminski G., Duffi E.M., Matsui T., Jorgensen W.L. 1994. Free energies of hydration and pure liquid properties of hydrocarbons from the OPLS all atom model. J. Phys. Chem. 98, 13077-13098.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 13077-13098
-
-
Kaminski, G.1
Duffi, E.M.2
Matsui, T.3
Jorgensen, W.L.4
-
50
-
-
0011134241
-
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
-
Halgren T.A. 1996. Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions. J. Comp. Chem. 17, 520-552.
-
(1996)
J. Comp. Chem.
, vol.17
, pp. 520-552
-
-
Halgren, T.A.1
-
51
-
-
0000999989
-
Combined Ab Initio/Empirical approach for optimization of Lennard-Jones parameters
-
Yin D., Mackerell A.D.J. 1998. Combined Ab Initio/Empirical approach for optimization of Lennard-Jones parameters. J. Comp. Chem. 18, 334-348.
-
(1998)
J. Comp. Chem.
, vol.18
, pp. 334-348
-
-
Yin, D.1
Mackerell, A.D.J.2
-
52
-
-
0001578237
-
CHARMM92 force field for biomolecular simulations
-
Smith J.C., Karplus M.J. 1994. CHARMM92 force field for biomolecular simulations. J. Am. Chem. Soc. 114, 801-819.
-
(1994)
J. Am. Chem. Soc.
, vol.114
, pp. 801-819
-
-
Smith, J.C.1
Karplus, M.J.2
-
54
-
-
0000116495
-
Thermodynamic properties of the Williams, OPLS-AA, and MMFF94 all-atom force fields for alkanes
-
Chen B., Marthin M.G., Siepman J.I. 1998. Thermodynamic properties of the Williams, OPLS-AA, and MMFF94 all-atom force fields for alkanes. J. Phys. Chem. B102, 2578-2586.
-
(1998)
J. Phys. Chem.
, vol.B102
, pp. 2578-2586
-
-
Chen, B.1
Marthin, M.G.2
Siepman, J.I.3
-
55
-
-
0030745939
-
Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assesment of empirial force field
-
Beachy M.D., Chasman D., Murphy R.B., Halgren T.H., Friesner R.A. 1997. Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assesment of empirial force field. J. Am. Chem. Soc. 119, 5908-5920.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 5908-5920
-
-
Beachy, M.D.1
Chasman, D.2
Murphy, R.B.3
Halgren, T.H.4
Friesner, R.A.5
-
56
-
-
0041967950
-
CFF95 force field development
-
Maple J.R., Hwang M.-J., Stockfisch T.P., Dinur U., Waldman M., Ewig C.S., Hagler A.T. 1994. CFF95 force field development. J. Am. Chem. Soc. 115, 162-176.
-
(1994)
J. Am. Chem. Soc.
, vol.115
, pp. 162-176
-
-
Maple, J.R.1
Hwang, M.-J.2
Stockfisch, T.P.3
Dinur, U.4
Waldman, M.5
Ewig, C.S.6
Hagler, A.T.7
-
58
-
-
33747333722
-
-
Russian source
-
-
-
-
59
-
-
0343213055
-
Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical QM methods (AM1, MNDO/M, PM3), and ab initio HF methods for interaction of DNA bases: Comparision with nonempirical beyond HF results
-
Hobza P., Kabelac M., Sponer J., Mejzlik P., Vondrasek J. 1997. Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical QM methods (AM1, MNDO/M, PM3), and ab initio HF methods for interaction of DNA bases: comparision with nonempirical beyond HF results. J. Comp. Chem. 18, 1137-1150.
-
(1997)
J. Comp. Chem.
, vol.18
, pp. 1137-1150
-
-
Hobza, P.1
Kabelac, M.2
Sponer, J.3
Mejzlik, P.4
Vondrasek, J.5
-
60
-
-
0032459726
-
Molecular dynamic simulations of environment and sequence dependent DNA conformations: The development of the BMS nucleic acid force field and comparison with experimental results
-
Langley D.R. 1998. Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results. J. Biomol. Struct. Dyn. 16, 487-509.
-
(1998)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 487-509
-
-
Langley, D.R.1
-
61
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe A., Maccerell A.D. Jr. 2000. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comp. Chem. 21, 86-104.
-
(2000)
J. Comp. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, A.1
Maccerell Jr., A.D.2
-
62
-
-
0000214231
-
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
-
Foloppe A., Maccerell A.D. Jr. 2000. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J. Comp. Chem. 21, 104-120.
-
(2000)
J. Comp. Chem.
, vol.21
, pp. 104-120
-
-
Foloppe, A.1
Maccerell Jr., A.D.2
-
63
-
-
33747373450
-
-
Russian source
-
-
-
-
64
-
-
33747345529
-
-
Russian source
-
-
-
-
65
-
-
33747366799
-
-
Russian source
-
-
-
-
66
-
-
33747331513
-
-
Russian source
-
-
-
-
68
-
-
0028484011
-
The spartial structure in liquid water
-
Kusalik P.G., Svishchev I.M. 1994. The spartial structure in liquid water. Science. 265, 1219-1221.
-
(1994)
Science
, vol.265
, pp. 1219-1221
-
-
Kusalik, P.G.1
Svishchev, I.M.2
-
69
-
-
0000125216
-
Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt M., Hirshberg M., Sharon R., Laiding K.E., Daggett V. 1997. Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution. J. Phys. Chem. B101, 5051-5061.
-
(1997)
J. Phys. Chem.
, vol.B101
, pp. 5051-5061
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Laiding, K.E.4
Daggett, V.5
-
72
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
73
-
-
0000035913
-
Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximun density
-
Jorgensen W.L., Jenson C. 1998. Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: seeking temperatures of maximun density. J. Comp. Chem. 19, 1179-1186.
-
(1998)
J. Comp. Chem.
, vol.19
, pp. 1179-1186
-
-
Jorgensen, W.L.1
Jenson, C.2
-
74
-
-
0000315458
-
Sensitivity analysis of distribution functions of liquid water
-
Zhu S.-B., Wong C.F. 1993. Sensitivity analysis of distribution functions of liquid water. J. Chem. Phys. 99, 9047-9052.
-
(1993)
J. Chem. Phys.
, vol.99
, pp. 9047-9052
-
-
Zhu, S.-B.1
Wong, C.F.2
-
77
-
-
0000042113
-
Ion solvation in polarizable water: Molecular dynamics simulations
-
Dang L.X., Rice J.E., Caldwell J., Kollman P.A. 1991. Ion solvation in polarizable water: molecular dynamics simulations. J. Am. Chem. Soc. 113, 2481-2486.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 2481-2486
-
-
Dang, L.X.1
Rice, J.E.2
Caldwell, J.3
Kollman, P.A.4
-
78
-
-
0000651116
-
Molecular dynamics study of water clusters, liquid, and liquid-vapor interface of water with many-body potentials
-
Dang L.X., Chang T.-S. 1997. Molecular dynamics study of water clusters, liquid, and liquid-vapor interface of water with many-body potentials. J. Chem. Phys. 106, 8149-8159.
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 8149-8159
-
-
Dang, L.X.1
Chang, T.-S.2
-
79
-
-
0000337544
-
Effective potentials for liquid water using polarizable and nonpolarizable models
-
Wallqvist A., Berne B.J. 1993. Effective potentials for liquid water using polarizable and nonpolarizable models. J. Phys. Chem. 97, 13841-13851.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 13841-13851
-
-
Wallqvist, A.1
Berne, B.J.2
-
80
-
-
0001475763
-
Distributed multipole analysis, or how to describe a molecular charge distribution
-
Stone A.J. 1981. Distributed multipole analysis, or how to describe a molecular charge distribution. Chem. Phys. Lett. 83, 233-237.
-
(1981)
Chem. Phys. Lett.
, vol.83
, pp. 233-237
-
-
Stone, A.J.1
-
81
-
-
84943840245
-
Towards an accurate intermolecular potential for water
-
Millot C., Stone A.J. 1992. Towards an accurate intermolecular potential for water. Mol. Phys. 77, 439-462.
-
(1992)
Mol. Phys.
, vol.77
, pp. 439-462
-
-
Millot, C.1
Stone, A.J.2
-
82
-
-
84947640036
-
Distributed multipole analysis methods and applications
-
Stone A.J., Alderton M. 1985. Distributed multipole analysis methods and applications. Mol. Phys. 56, 1047-1064.
-
(1985)
Mol. Phys.
, vol.56
, pp. 1047-1064
-
-
Stone, A.J.1
Alderton, M.2
-
83
-
-
33846823909
-
Particle meash Ewald: An N log(N) method for Ewald sums in large systems
-
Darden T., York D., Pedersen L. 1993. Particle meash Ewald: an N log(N) method for Ewald sums in large systems. J. Phys. Chem. 98, 10089-10092.
-
(1993)
J. Phys. Chem.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
84
-
-
0002997010
-
A comparision of particle-particle and particle meash and Ewald methods for calculating interactions in periodic molecular systems
-
Lutty B.A., Davis M.E., Tironi I.G., Van Gunsteren W.F. 1994. A comparision of particle-particle and particle meash and Ewald methods for calculating interactions in periodic molecular systems. Mol. Simul. 14, 11-20.
-
(1994)
Mol. Simul.
, vol.14
, pp. 11-20
-
-
Lutty, B.A.1
Davis, M.E.2
Tironi, I.G.3
Van Gunsteren, W.F.4
-
85
-
-
33645961739
-
A smooth particle-meash Ewald method
-
Essmann U., Perera L., Berkowitz L., Darden T., Lee H., Pedersen L.G. 1995. A smooth particle-meash Ewald method. J. Phys. Chem. 103, 8577-8593.
-
(1995)
J. Phys. Chem.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
86
-
-
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. USA. 117, 5000-5002.
-
(1995)
J. Am. Chem. Soc. USA
, vol.117
, pp. 5000-5002
-
-
York, D.M.1
Yang, W.2
Lee, H.3
Darden, T.4
Pedersen, L.G.5
-
88
-
-
0000952715
-
Effect of periodic box size on aqueous molecular dynamics simulation of DNA dodecamer with particle-meash Ewald method
-
Souza O.N., Ornstein R. 1997. Effect of periodic box size on aqueous molecular dynamics simulation of DNA dodecamer with particle-meash Ewald method. Biophys. J. 72, 2395-2397.
-
(1997)
Biophys. J.
, vol.72
, pp. 2395-2397
-
-
Souza, O.N.1
Ornstein, R.2
-
89
-
-
0031566427
-
RNA hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(asp) anicodon hairpin
-
Auffinger P., Westhof E. 1997. RNA hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(asp) anicodon hairpin. J. Mol. Biol. 269, 326-341.
-
(1997)
J. Mol. Biol.
, vol.269
, pp. 326-341
-
-
Auffinger, P.1
Westhof, E.2
-
90
-
-
0029170114
-
Molecular dynamics simulations on solvated biomolecular systems: The particle meash Ewald method leads to stable trajectories of DNA, RNA, and proteins
-
Cheatham T.E., Miller J.K., Fox T., Darden T.A., Kollman P.A. 1995. Molecular dynamics simulations on solvated biomolecular systems: the particle meash Ewald method leads to stable trajectories of DNA, RNA, and proteins. J. Am. Chem. Soc. USA. 117, 4193-4194.
-
(1995)
J. Am. Chem. Soc. USA
, vol.117
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.K.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
91
-
-
0031834850
-
Importance of explicit ions for protein stability
-
Ibragimova G.T., Wade R.C. 1998. Importance of explicit ions for protein stability. Biophys. J. 74, 2906-2911.
-
(1998)
Biophys. J.
, vol.74
, pp. 2906-2911
-
-
Ibragimova, G.T.1
Wade, R.C.2
-
92
-
-
0038683517
-
Ewald artifacts in computer simulstions of ionic solvation and ion-ion interaction: A continuum electrostatic study
-
Hunenberger P.H., McCammon J.A. 1999. Ewald artifacts in computer simulstions of ionic solvation and ion-ion interaction: a continuum electrostatic study. J. Chem. Phys. 110, 1858-1872.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 1858-1872
-
-
Hunenberger, P.H.1
McCammon, J.A.2
-
93
-
-
0037627173
-
Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatic study
-
Hunenberger P.H., McCammon J.A. 1999. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatic study. Biophys. Chem. 78, 69-88.
-
(1999)
Biophys. Chem.
, vol.78
, pp. 69-88
-
-
Hunenberger, P.H.1
McCammon, J.A.2
-
94
-
-
36449001478
-
Molecular dynamics algorithm for multiple time scales: System with long range forces
-
Tuckerman M.E., Berne B.J., Rossi A. 1991. Molecular dynamics algorithm for multiple time scales: system with long range forces. J. Chem. Phys. 97, 6811-6815.
-
(1991)
J. Chem. Phys.
, vol.97
, pp. 6811-6815
-
-
Tuckerman, M.E.1
Berne, B.J.2
Rossi, A.3
-
95
-
-
33646650705
-
Reversible multiple time scale molecular dynamics
-
Tuckerman M.E., Berne B.J., Rossi A. 1992. Reversible multiple time scale molecular dynamics. J. Chem. Phys. 97, 1990-2001.
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 1990-2001
-
-
Tuckerman, M.E.1
Berne, B.J.2
Rossi, A.3
-
96
-
-
0000695661
-
Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they?
-
Grubmuller H., Tavan P. 1998. Multiple time step algorithms for molecular dynamics simulations of proteins: how good are they? J. Comp. Chem. 19, 1534-1552.
-
(1998)
J. Comp. Chem.
, vol.19
, pp. 1534-1552
-
-
Grubmuller, H.1
Tavan, P.2
-
97
-
-
0003085194
-
Canonical numerical methods for molecular dynamic simulations
-
Okonbor D.I., Skeel R.D. 1994. Canonical numerical methods for molecular dynamic simulations. J. Comp. Chem. 15, 72-79.
-
(1994)
J. Comp. Chem.
, vol.15
, pp. 72-79
-
-
Okonbor, D.I.1
Skeel, R.D.2
-
98
-
-
24844474730
-
A very fast molecular dynamics method to simulate biomolecular systems with electrostatic interactions
-
Procacci P., Darden T., Marchi M. 1996. A very fast molecular dynamics method to simulate biomolecular systems with electrostatic interactions. J. Phys. Chem. 100, 10464-10468.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 10464-10468
-
-
Procacci, P.1
Darden, T.2
Marchi, M.3
-
99
-
-
0031872292
-
Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamic simulations with explicit solvent, and an implicit solvent continuum model
-
Vorobjev Y.N., Almagro J.C., Hermans J. 1998. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamic simulations with explicit solvent, and an implicit solvent continuum model. Proteins: Struct. Func. Gen. 32, 399-413.
-
(1998)
Proteins: Struct. Func. Gen.
, vol.32
, pp. 399-413
-
-
Vorobjev, Y.N.1
Almagro, J.C.2
Hermans, J.3
-
100
-
-
0033003955
-
ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit continuum model
-
Vorobjev Y.N., Hermans J. 1999. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit continuum model. Biophys. Chem. 78, 195-205.
-
(1999)
Biophys. Chem.
, vol.78
, pp. 195-205
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
101
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff D., Sharp K.A., Honig B. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98, 1978-1988.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
102
-
-
0000043930
-
Solvation free energy of biomacromolecules: Parameters for a modified generalized bom model consistent with the AMBER force field
-
Jayaram B., Sprous D., Beveridge D.L. 1998. Solvation free energy of biomacromolecules: parameters for a modified generalized bom model consistent with the AMBER force field. J. Phys. Chem. 102, 9571-9576.
-
(1998)
J. Phys. Chem.
, vol.102
, pp. 9571-9576
-
-
Jayaram, B.1
Sprous, D.2
Beveridge, D.L.3
-
103
-
-
0001246294
-
Generalized Born model based on a surface integral formulation
-
Ghosh A., Rapp C.S., Friesner R.A. 1998. Generalized Born model based on a surface integral formulation. J. Phys. Chem. B102, 10983-10990.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 10983-10990
-
-
Ghosh, A.1
Rapp, C.S.2
Friesner, R.A.3
-
104
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate DNA helices
-
Srinivasan J., Cheatham T.E. III, Cieplak P., Kollman P.A., Case D.A. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate DNA helices. J. Am. Chem. Soc. 120, 9401-9409.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham III, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
105
-
-
0035186285
-
Free energy of protein decoys provide insight into determinants of protein stability
-
Vorobjev Y.N., Hermans J. 2001. Free energy of protein decoys provide insight into determinants of protein stability. Protein Sci. 10, 2498-2506.
-
(2001)
Protein Sci.
, vol.10
, pp. 2498-2506
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
106
-
-
0031788539
-
Molecular dynamic and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
-
Cheatham T.E. III, Srinivasan J., Case D., Kollman P.A. 1999. Molecular dynamic and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 16, 265-280.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 265-280
-
-
Cheatham III, T.E.1
Srinivasan, J.2
Case, D.3
Kollman, P.A.4
-
107
-
-
0032556243
-
Free energy analysis of the conformational preferences of a and B forms of DNA in solution
-
Jayaram B., Sprous D., Young M.A., Beveridge D.L. 1998. Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J. Am. Chem. Soc. 120, 10629-10633.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 10629-10633
-
-
Jayaram, B.1
Sprous, D.2
Young, M.A.3
Beveridge, D.L.4
-
108
-
-
0001101548
-
Free energy analysis of protein-DNA binding: The EcoRI Endonuclease-DNA complex
-
Jayaram B., McConnell K.J., Dixit S.B., Beveridge DL. 1999. Free energy analysis of protein-DNA binding: the EcoRI Endonuclease-DNA complex. J. Comp. Phys. 151, 333-357.
-
(1999)
J. Comp. Phys.
, vol.151
, pp. 333-357
-
-
Jayaram, B.1
McConnell, K.J.2
Dixit, S.B.3
Beveridge, D.L.4
-
109
-
-
0033468737
-
Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects
-
Srinivasan J., Trevathan M.W., Beroza P., Case D.A. 1999. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects. Theor. Chem. Acc. 101, 426-434.
-
(1999)
Theor. Chem. Acc.
, vol.101
, pp. 426-434
-
-
Srinivasan, J.1
Trevathan, M.W.2
Beroza, P.3
Case, D.A.4
-
111
-
-
0033135638
-
Effective energy function for protein in solution
-
Lazaridis T., Karplus M. 1999. Effective energy function for protein in solution. Proteins: Struct. Func. Gen. 35, 133-152.
-
(1999)
Proteins: Struct. Func. Gen.
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
112
-
-
0037080244
-
Rapid grid-based construction of the molecular surface and use of induced surface charge to calculate reaction field energies
-
Rocchia W., Sridharan S., Nicholls A., Alexov E., Chiabrera A., Honig B. 2002. Rapid grid-based construction of the molecular surface and use of induced surface charge to calculate reaction field energies. J. Comp. Chem. 23, 128-137.
-
(2002)
J. Comp. Chem.
, vol.23
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
Alexov, E.4
Chiabrera, A.5
Honig, B.6
-
114
-
-
0029075795
-
The essential dynamics of thermolysin: Confirmation of hinge-bending motion
-
Van Aalten D.M.F., Amadei A., Linssen A.B.M., Eijsink V.G.H., Vriend G., Berendsen H.J.C. 1995. The essential dynamics of thermolysin: confirmation of hinge-bending motion. Proteins: Struct. Funct. Gen. 22, 45-54.
-
(1995)
Proteins: Struct. Funct. Gen.
, vol.22
, pp. 45-54
-
-
Van Aalten, D.M.F.1
Amadei, A.2
Linssen, A.B.M.3
Eijsink, V.G.H.4
Vriend, G.5
Berendsen, H.J.C.6
-
115
-
-
0029985860
-
An efficient method for sampling the essential subspace of proteins
-
Amadei A., Linssen A.B.M., De Groot B.M., Van Aalten D.M.F., Berendsen H.J.C. 1996. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn. 13, 615-626.
-
(1996)
J. Biomol. Struct. Dyn.
, vol.13
, pp. 615-626
-
-
Amadei, A.1
Linssen, A.B.M.2
De Groot, B.M.3
Van Aalten, D.M.F.4
Berendsen, H.J.C.5
-
116
-
-
0000885331
-
Harmonic analysis of large systems. I. Methodology
-
Brooks B.R., Janezic D., Karplus M. 1995. Harmonic analysis of large systems. I. Methodology. J. Comp. Chem. 16, 1522-1542.
-
(1995)
J. Comp. Chem.
, vol.16
, pp. 1522-1542
-
-
Brooks, B.R.1
Janezic, D.2
Karplus, M.3
-
117
-
-
84986469420
-
Harmonic analysis of large systems. II. Comparison of different protein models
-
Janezic D., Brooks B.R. 1995. Harmonic analysis of large systems. II. Comparison of different protein models. J. Comp. Chem. 16, 1543-1553.
-
(1995)
J. Comp. Chem.
, vol.16
, pp. 1543-1553
-
-
Janezic, D.1
Brooks, B.R.2
-
118
-
-
84986473952
-
Harmonic analysis of large systems. III. Comparison with molecular dynamics
-
Janezic D., Venable R.M., Brooks B.R. 1995. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J. Comp. Chem. 16, 1554-1566.
-
(1995)
J. Comp. Chem.
, vol.16
, pp. 1554-1566
-
-
Janezic, D.1
Venable, R.M.2
Brooks, B.R.3
-
119
-
-
0033618122
-
Molecular dynamics studies of DNA Atract structure and flexibility
-
Sherer E.C., Harris S.A., Soliva R., Orozco M., Laughton C.A. 1999. Molecular dynamics studies of DNA Atract structure and flexibility. J. Am. Chem. Soc. 121, 5981-5991.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 5981-5991
-
-
Sherer, E.C.1
Harris, S.A.2
Soliva, R.3
Orozco, M.4
Laughton, C.A.5
-
120
-
-
0030862276
-
A 5-nanosecond molecular dynamics trajectory for B-DNA: Analysis of structure, motions and solvation
-
Young M.A., Ravishanker G., Beveridge D.L. 1997. A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions and solvation. Biophys. J. 73, 2313-2336.
-
(1997)
Biophys. J.
, vol.73
, pp. 2313-2336
-
-
Young, M.A.1
Ravishanker, G.2
Beveridge, D.L.3
-
121
-
-
0000216904
-
Local dielectric environment of B-DNA in solution: Results from a 14 nanosecond molecular dynamics trajectory
-
Young M.A., Jayaram B., Beveridge D.L. 1998. Local dielectric environment of B-DNA in solution: results from a 14 nanosecond molecular dynamics trajectory. J. Phys. Chem. B102, 7666-7669.
-
(1998)
J. Phys. Chem.
, vol.B102
, pp. 7666-7669
-
-
Young, M.A.1
Jayaram, B.2
Beveridge, D.L.3
-
122
-
-
0000115258
-
Molecular dynamics studies of the conformational preferences of a DNA double helix in water and in an ethanol/water mixture: Theoretical considerations of the A/B transition
-
Sprous D., Young M.A., Beveridge D.L. 1998. Molecular dynamics studies of the conformational preferences of a DNA double helix in water and in an ethanol/water mixture: theoretical considerations of the A/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
-
124
-
-
0029006896
-
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes
-
Young M.A., Ravishanker G., Beveridge D.L., Berman H.M. 1995. 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
-
125
-
-
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., Srinivasan J., Goljer I., Kumar S., Beveridge D.L., Bolton P.H. 1995. 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). Meth. Enzymology. 261, 121-144.
-
(1995)
Meth. Enzymology
, 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
-
126
-
-
0031552364
-
X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract dependent curvature
-
Shatzky-Schwatz M., Arbuckle N., Eisenstein M., Rabinovich D., Bareket-Samish A., Haran T.E., Luisi B.F., Shakked Z. 1997. X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract dependent curvature. J. Mol. Biol. 267, 595-623.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 595-623
-
-
Shatzky-Schwatz, M.1
Arbuckle, N.2
Eisenstein, M.3
Rabinovich, D.4
Bareket-Samish, A.5
Haran, T.E.6
Luisi, B.F.7
Shakked, Z.8
-
127
-
-
0032922174
-
A modified version of the force field with improved sugar pucker phases and helical repeat
-
Cheatham T.E. III, Cieplak P., Kollman P.A. 1999. A modified version of the force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16, 845-862.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 845-862
-
-
Cheatham III, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
128
-
-
0034682870
-
A-tract bending: Insights into experimental structures by computational models
-
Strahs D., Schlick T. 2000. A-tract bending: insights into experimental structures by computational models. J. Mol. Biol. 301, 643-663.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 643-663
-
-
Strahs, D.1
Schlick, T.2
-
130
-
-
0029911794
-
Asp: Structuring effects of C-H O hydrogen bonds and of long-range hydration forces
-
Asp: structuring effects of C-H O hydrogen bonds and of long-range hydration forces. J. Am. Chem. Soc. 118, 1181-1189.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 1181-1189
-
-
Auffinger, P.1
Louise-May, S.2
Westhof, E.3
-
131
-
-
0029776466
-
Asp anticodon hairpin: 3 ns of multiple molecular dynamics simulations
-
Asp anticodon hairpin: 3 ns of multiple molecular dynamics simulations. Biophys. J. 71, 940-954.
-
(1996)
Biophys. J.
, vol.71
, pp. 940-954
-
-
Auffinger, P.1
Westhof, E.2
-
132
-
-
0030723027
-
Rules governing the orientation of the 2́ hydroxyl groupi RNA
-
Auffinger P., Westhof E. 1997. Rules governing the orientation of the 2́ hydroxyl groupi RNA. J. Mol. Biol. 274, 54-63.
-
(1997)
J. Mol. Biol.
, vol.274
, pp. 54-63
-
-
Auffinger, P.1
Westhof, E.2
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