-
1
-
-
0001200075
-
End effects in electrostatic potentials of cylinders: Models for DNA fragments
-
Allison SA. 1994. End effects in electrostatic potentials of cylinders: models for DNA fragments. J. Phys. Chem. 98:12091
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 12091
-
-
Allison, S.A.1
-
3
-
-
0025308916
-
Ionic distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications
-
Anderson CF, Record MT Jr. 1990. Ionic distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. Annu. Rev. Biophys. Biophys. Chem. 19:423
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 423
-
-
Anderson, C.F.1
Record Jr., M.T.2
-
4
-
-
0000144150
-
Salt dependence of oligoion-polyion binding: A thermodynamic description based on preferential interaction coefficients
-
3a. Anderson C, Record MT. 1993. Salt dependence of oligoion-polyion binding: a thermodynamic description based on preferential interaction coefficients. J. Phys. Chem. 97:7116
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 7116
-
-
Anderson, C.1
Record, M.T.2
-
5
-
-
0000836584
-
Ionic atmosphere of rod-like polyelectrolytes. A hypernetted chain study
-
Bacquet R, Rossky PJ. 1984. Ionic atmosphere of rod-like polyelectrolytes. A hypernetted chain study. J. Phys. Chem. 88:2660
-
(1984)
J. Phys. Chem.
, vol.88
, pp. 2660
-
-
Bacquet, R.1
Rossky, P.J.2
-
6
-
-
0000533571
-
Ionic distributions and competitive association in DNA/mixed salt solutions
-
Bacquet RJ, Rossky PJ. 1988. Ionic distributions and competitive association in DNA/mixed salt solutions. J. Phys. Chem. 92:3604
-
(1988)
J. Phys. Chem.
, vol.92
, pp. 3604
-
-
Bacquet, R.J.1
Rossky, P.J.2
-
7
-
-
36749121933
-
Theory of twisting and bending of chain macromolecules: Analysis of the fluorescence depolarization of DNA
-
Barkley MD, Zimm BH. 1979. Theory of twisting and bending of chain macromolecules: analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70:2991
-
(1979)
J. Chem. Phys.
, vol.70
, pp. 2991
-
-
Barkley, M.D.1
Zimm, B.H.2
-
8
-
-
0000339209
-
Electrostatic effects in biological molecules
-
Bashford D. 1991. Electrostatic effects in biological molecules. Curr. Opin. Struct. Biol. 1:175
-
(1991)
Curr. Opin. Struct. Biol.
, vol.1
, pp. 175
-
-
Bashford, D.1
-
11
-
-
0026742978
-
The Nucleic Acid Database: A comprehensive relational database of three dimensional structures of nucleic acids
-
Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, et al. 1992. The Nucleic Acid Database: a comprehensive relational database of three dimensional structures of nucleic acids. Biophys. J. 63:751
-
(1992)
Biophys. J.
, vol.63
, pp. 751
-
-
Berman, H.M.1
Olson, W.K.2
Beveridge, D.L.3
Westbrook, J.4
Gelbin, A.5
-
12
-
-
0017411710
-
The Protein Data Bank: A computer-based archive file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, et al. 1977. The Protein Data Bank: a computer-based archive file for macromolecular structures. J. Mol. Biol. 112:535
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer Jr., E.F.4
Brice, M.D.5
-
13
-
-
0024578173
-
Free energy via molecular simulation: Applications to chemical and biomolecular systems
-
Beveridge DL, Dicapua FM. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431
-
(1989)
Annu. Rev. Biophys. Biophys. Chem.
, vol.18
, pp. 431
-
-
Beveridge, D.L.1
Dicapua, F.M.2
-
14
-
-
0021742769
-
Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies
-
Beveridge DL, Maye PV, Jayaram B, Ravishanker G, Mezei M. 1984. Aqueous hydration of nucleic acid constituents: Monte Carlo computer simulation studies. J. Biomol. Struct. Dyn. 2:261
-
(1984)
J. Biomol. Struct. Dyn.
, vol.2
, pp. 261
-
-
Beveridge, D.L.1
Maye, P.V.2
Jayaram, B.3
Ravishanker, G.4
Mezei, M.5
-
16
-
-
0009698591
-
-
ed. DL Beveridge, R Lavery, Schenectady, NY: Adenine
-
Beveridge DL, Subramanian PS, Jayaram B, Swaminathan S. 1990. In Theoretical Biochemistry and Molecular Biophysics, ed. DL Beveridge, R Lavery, pp. 17-38. Schenectady, NY: Adenine
-
(1990)
Theoretical Biochemistry and Molecular Biophysics
, pp. 17-38
-
-
Beveridge, D.L.1
Subramanian, P.S.2
Jayaram, B.3
Swaminathan, S.4
-
17
-
-
0002593973
-
Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers
-
ed. E Westhof, London: Macmillan
-
Beveridge DL, Swaminathan S, Ravishanker G, Whitka JM, Srinivasan J, et al. 1993. Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers. In Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers in Water and Biological Molecules, ed. E Westhof, pp. 165-225. London: Macmillan
-
(1993)
Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers in Water and Biological Molecules
, pp. 165-225
-
-
Beveridge, D.L.1
Swaminathan, S.2
Ravishanker, G.3
Whitka, J.M.4
Srinivasan, J.5
-
18
-
-
0000806644
-
Sodium-23 nuclear magnetic resonance studies of cation-deoxyribonucleic acid interactions
-
Bleam ML, Anderson CF, Record MT Jr. 1983. Sodium-23 nuclear magnetic resonance studies of cation-deoxyribonucleic acid interactions. Biochemistry 22:5418
-
(1983)
Biochemistry
, vol.22
, pp. 5418
-
-
Bleam, M.L.1
Anderson, C.F.2
Record Jr., M.T.3
-
19
-
-
0026253815
-
Condensation of DNA by multivalent cations: Considerations on mechanism
-
Bloomfield VA. 1991. Condensation of DNA by multivalent cations: considerations on mechanism. Biopolymers 31:1471
-
(1991)
Biopolymers
, vol.31
, pp. 1471
-
-
Bloomfield, V.A.1
-
20
-
-
0028030641
-
Conformational transitions of duplex and triplex nucleic acid helices: Thermodynamic analysis of the effects of salt concentration on stability using preferential interaction coefficients
-
18a. Bond JP, Anderson CF, Record MT. 1994. Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of the effects of salt concentration on stability using preferential interaction coefficients. Biophys. J. 67:825
-
(1994)
Biophys. J.
, vol.67
, pp. 825
-
-
Bond, J.P.1
Anderson, C.F.2
Record, M.T.3
-
21
-
-
0025924787
-
1H NMR study of the base-pairing reaction of d(GGAATTCC): Salt effects on the equilibria and kinetics of strand association
-
1H NMR study of the base-pairing reaction of d(GGAATTCC): salt effects on the equilibria and kinetics of strand association. Biochemistry 30: 754
-
(1991)
Biochemistry
, vol.30
, pp. 754
-
-
Braunlin, W.H.1
Bloomfield, V.A.2
-
22
-
-
0000583619
-
Evidence for the stochastic nature of base pair opening in DNA. A Brownian dynamics simulation
-
Briki F, Ramstein J, Lavery R, Genest D. 1991. Evidence for the stochastic nature of base pair opening in DNA. A Brownian dynamics simulation. J. Am. Chem. Soc. 113:2490
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 2490
-
-
Briki, F.1
Ramstein, J.2
Lavery, R.3
Genest, D.4
-
23
-
-
0023140814
-
Crystallographic R factor refinement by molecular dynamics
-
Bruenger A, Kuriyan J, Karplus M. 1987. Crystallographic R factor refinement by molecular dynamics. Science 235:458
-
(1987)
Science
, vol.235
, pp. 458
-
-
Bruenger, A.1
Kuriyan, J.2
Karplus, M.3
-
24
-
-
0027554810
-
A model for the dynemicin-A cleavage of DNA using molecular dynamics simulation
-
Cardozo MG, Hopfinger AJ. 1993. A model for the dynemicin-A cleavage of DNA using molecular dynamics simulation. Biopolymers 33:377
-
(1993)
Biopolymers
, vol.33
, pp. 377
-
-
Cardozo, M.G.1
Hopfinger, A.J.2
-
25
-
-
0001373924
-
Measurements of monovalent and divalent counterion distributions around persistence length DNA fragments in solution
-
Chang S-L, Chen S-H, Rill RL, Lin JS. 1990. Measurements of monovalent and divalent counterion distributions around persistence length DNA fragments in solution. J. Phys. Chem. 94:8025
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8025
-
-
Chang, S.-L.1
Chen, S.-H.2
Rill, R.L.3
Lin, J.S.4
-
26
-
-
0029170114
-
Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins
-
Cheatham TE III, Miller JL, Fox T, Darden TA, Kollman PA. 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
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4193
-
-
Cheatham III, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
28
-
-
0028184699
-
Kinetics of supercoiling studied by Brownian dynamics simulation
-
Chirico G, Langowski J. 1994. Kinetics of supercoiling studied by Brownian dynamics simulation. Biopolymers 34:415
-
(1994)
Biopolymers
, vol.34
, pp. 415
-
-
Chirico, G.1
Langowski, J.2
-
29
-
-
0025308014
-
Free energy calculation of base specificity of drug-DNA interactions: Application to daunomycin and acridine intercalation into DNA
-
Cieplak P, Rao SN, Grootenhuis PDJ, Kollman PA. 1990. Free energy calculation of base specificity of drug-DNA interactions: application to daunomycin and acridine intercalation into DNA. Biopolymers 29: 717
-
(1990)
Biopolymers
, vol.29
, pp. 717
-
-
Cieplak, P.1
Rao, S.N.2
Grootenhuis, P.D.J.3
Kollman, P.A.4
-
30
-
-
0024116002
-
Ions around DNA: Monte Carlo estimates of distribution with improved electrostatic potentials
-
Conrad J, Troll M, Zimm BH. 1988. Ions around DNA: Monte Carlo estimates of distribution with improved electrostatic potentials. Biopolymers 27:1711
-
(1988)
Biopolymers
, vol.27
, pp. 1711
-
-
Conrad, J.1
Troll, M.2
Zimm, B.H.3
-
31
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids and organic molecules
-
28a. Cornell WD, Cieplak P, Bayly CI, Gould IA, et al. 1995. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117: 5179
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.A.4
-
32
-
-
33645085472
-
Modified Poisson-Boltzmann theory applied to linear polyelectrolyte solutions
-
Das T, Bratko D, Bhuiyan LB, Outhwaite CW. 1995. Modified Poisson-Boltzmann theory applied to linear polyelectrolyte solutions. J. Phys. Chem. 99:410
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 410
-
-
Das, T.1
Bratko, D.2
Bhuiyan, L.B.3
Outhwaite, C.W.4
-
33
-
-
4243463817
-
Electrostatics in biomolecular structure and dynamics
-
Davis ME, McCammon JA. 1990. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90: 509
-
(1990)
Chem. Rev.
, vol.90
, pp. 509
-
-
Davis, M.E.1
McCammon, J.A.2
-
34
-
-
0019843568
-
Structure of a B-DNA dodecamer. III. Geometry of hydration
-
Drew HR, Dickerson RE. 1981. Structure of a B-DNA dodecamer. III. Geometry of hydration. J. Mol. Biol. 151:535
-
(1981)
J. Mol. Biol.
, vol.151
, pp. 535
-
-
Drew, H.R.1
Dickerson, R.E.2
-
35
-
-
0027367276
-
Brownian dynamics simulations of probe and self-diffusion in concentrated protein and DNA solutions
-
31a. Dwyer JD, Bloomfield VA. 1993. Brownian dynamics simulations of probe and self-diffusion in concentrated protein and DNA solutions. Biophys. J. 65:1810
-
(1993)
Biophys. J.
, vol.65
, pp. 1810
-
-
Dwyer, J.D.1
Bloomfield, V.A.2
-
36
-
-
0027395303
-
Theoretical predictions of DNA hairpin-loop conformations. Correlations with thermodynamic and spectroscopic data
-
Erie DA, Suri AK, Breslauer KJ, Jones RA, Olson WK. 1993. Theoretical predictions of DNA hairpin-loop conformations. Correlations with thermodynamic and spectroscopic data. Biochemistry 32:436
-
(1993)
Biochemistry
, vol.32
, pp. 436
-
-
Erie, D.A.1
Suri, A.K.2
Breslauer, K.J.3
Jones, R.A.4
Olson, W.K.5
-
40
-
-
0000246675
-
Molecular dynamics studies of the behaviour of water molecules and small ions in concentrated solutions of polymeric B-DNA
-
Forester TR, McDonald IR. 1991. Molecular dynamics studies of the behaviour of water molecules and small ions in concentrated solutions of polymeric B-DNA. Mol. Phys. 72: 643
-
(1991)
Mol. Phys.
, vol.72
, pp. 643
-
-
Forester, T.R.1
McDonald, I.R.2
-
42
-
-
0026816545
-
The electrostatic contribution to DNA base-stacking interactions
-
Friedman R, Honig B. 1992. The electrostatic contribution to DNA base-stacking interactions. Biopolymers 32:145
-
(1992)
Biopolymers
, vol.32
, pp. 145
-
-
Friedman, R.1
Honig, B.2
-
43
-
-
12644309841
-
The polyelectrolyte correction to site exclusion numbers
-
ed. NR Kallenbach, Schenectady, NY: Adenine
-
Friedman RAG, Manning GS, Shahin MA. 1990. The polyelectrolyte correction to site exclusion numbers. In Drug-DNA Binding in Chemistry and Physics of DNA-Ligand Interactions, ed. NR Kallenbach, pp. 37-64. Schenectady, NY: Adenine
-
(1990)
Drug-DNA Binding in Chemistry and Physics of DNA-Ligand Interactions
, pp. 37-64
-
-
Friedman, R.A.G.1
Manning, G.S.2
Shahin, M.A.3
-
44
-
-
84986467024
-
Efficient conformational space sampling for nucleosides using internal coordinate Monte Carlo simulations and a modified furanose description
-
Gabb HA, Lavery R, Prevost C. 1995. Efficient conformational space sampling for nucleosides using internal coordinate Monte Carlo simulations and a modified furanose description. J. Comp. Chem. 16:667
-
(1995)
J. Comp. Chem.
, vol.16
, pp. 667
-
-
Gabb, H.A.1
Lavery, R.2
Prevost, C.3
-
45
-
-
0025231445
-
Netropsin binding to poly[d(ic)] poly-[d(IC)] and poly[d(GC)] poly-[d(GC)]: A computer simulation
-
Gago F, Richards WG. 1990. Netropsin binding to poly[d(ic)] poly-[d(IC)] and poly[d(GC)] poly-[d(GC)]: a computer simulation. Mol. Pharmacol. 37:341
-
(1990)
Mol. Pharmacol.
, vol.37
, pp. 341
-
-
Gago, F.1
Richards, W.G.2
-
46
-
-
0343757149
-
Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution
-
Garcia AE, Soumpasis DM. 1989. Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proc. Natl. Acad. Sci. USA 86:3160
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 3160
-
-
Garcia, A.E.1
Soumpasis, D.M.2
-
47
-
-
0347920629
-
Simulations of the counterion and solvent distribution functions around two simple models of a polyelectrolyte
-
Gordon HL, Goldman S. 1992. Simulations of the counterion and solvent distribution functions around two simple models of a polyelectrolyte. J. Phys. Chem. 96:1921
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 1921
-
-
Gordon, H.L.1
Goldman, S.2
-
48
-
-
0001828023
-
Interactions of polyelectrolytes with simple electrolytes. I. Theory for electrostatic potential and Donnan equilibrium for a cylindrical rod model: The effect of site-binding in chemical physics of ionic solutions
-
ed. BE Conway, RG Barradas, New York: Wiley & Sons
-
Gross LM, Strauss UP. 1966. Interactions of polyelectrolytes with simple electrolytes. I. Theory for electrostatic potential and Donnan equilibrium for a cylindrical rod model: the effect of site-binding in chemical physics of ionic solutions. In Chemical Physics of Ionic Solutions ed. BE Conway, RG Barradas, pp. 361-89. New York: Wiley & Sons
-
(1966)
Chemical Physics of Ionic Solutions
, pp. 361-389
-
-
Gross, L.M.1
Strauss, U.P.2
-
49
-
-
0026656556
-
A simple explanation of the electrostatics of the B to Z transition of DNA
-
Gueron M, Demaret J-P. 1992. A simple explanation of the electrostatics of the B to Z transition of DNA. Proc. Natl. Acad. Sci. USA 89:5740
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 5740
-
-
Gueron, M.1
Demaret, J.-P.2
-
50
-
-
84985698666
-
Polyelectrolyte theory. I. Counterion accumulation site binding and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations
-
Gueron M, Weisbuch G. 1980. Polyelectrolyte theory. I. Counterion accumulation site binding and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations. Biopolymers 19:353
-
(1980)
Biopolymers
, vol.19
, pp. 353
-
-
Gueron, M.1
Weisbuch, G.2
-
51
-
-
0001097403
-
Distribution and dynamics of mobile ions in systems of ordered B-DNA
-
Guldbrand LE, Forester TR, Lynden-Bell RM. 1989. Distribution and dynamics of mobile ions in systems of ordered B-DNA. Mol. Phys. 67:473
-
(1989)
Mol. Phys.
, vol.67
, pp. 473
-
-
Guldbrand, L.E.1
Forester, T.R.2
Lynden-Bell, R.M.3
-
52
-
-
0024519351
-
Treatment of electrostatic effects in macromolecular modeling
-
Harvey S. 1989. Treatment of electrostatic effects in macromolecular modeling. Proteins 5:78
-
(1989)
Proteins
, vol.5
, pp. 78
-
-
Harvey, S.1
-
53
-
-
0026563459
-
Physico chemical properties of 〉- vs (S)-methylphosphonate substitution on antisense DNA hybridization determined by free energy perturbation and molecular dynamics
-
Hausheer FH, Rao BG, Saxe JD, Singh UC. 1992. Physico chemical properties of 〉- vs (S)-methylphosphonate substitution on antisense DNA hybridization determined by free energy perturbation and molecular dynamics. J. Am. Chem. Soc. 114: 3201
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 3201
-
-
Hausheer, F.H.1
Rao, B.G.2
Saxe, J.D.3
Singh, U.C.4
-
54
-
-
21944448053
-
Electrostatic potentials near the surface of DNA: Comparing theory and experiment
-
Hecht JL, Honig B, Shin Y-K, Hubbell WL. 1995. Electrostatic potentials near the surface of DNA: comparing theory and experiment. J. Phys. Chem. 99:7782
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 7782
-
-
Hecht, J.L.1
Honig, B.2
Shin, Y.-K.3
Hubbell, W.L.4
-
55
-
-
84990406847
-
Dielectric effects in biopolymers: The theory of ionic saturation revisited
-
Hingerty BE, Ritchie RH, Ferrell TL, Turner JE. 1985. Dielectric effects in biopolymers: the theory of ionic saturation revisited. Biopolymers 24:427
-
(1985)
Biopolymers
, vol.24
, pp. 427
-
-
Hingerty, B.E.1
Ritchie, R.H.2
Ferrell, T.L.3
Turner, J.E.4
-
56
-
-
0347696834
-
Salt induced conformational changes in DNA: Analysis using the polymer RISM theory
-
Hirata F, Levy RM. 1989. Salt induced conformational changes in DNA: analysis using the polymer RISM theory. J. Phys. Chem. 93:479
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 479
-
-
Hirata, F.1
Levy, R.M.2
-
57
-
-
0028092707
-
Protein electrostatics - Rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation
-
51a. Holst M, Kozack R, Saied F. 1994. Protein electrostatics - rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation. J. Biomol. Struct. Dyn. 11:1437
-
(1994)
J. Biomol. Struct. Dyn.
, vol.11
, pp. 1437
-
-
Holst, M.1
Kozack, R.2
Saied, F.3
-
58
-
-
0000525721
-
Multigrid solution of the Poisson-Boltzmann equation
-
51b. Holst M, Saied F. 1993. Multigrid solution of the Poisson-Boltzmann equation. J. Comp. Chem. 14:105
-
(1993)
J. Comp. Chem.
, vol.14
, pp. 105
-
-
Holst, M.1
Saied, F.2
-
59
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig B, Nicholls A. 1995. Classical electrostatics in biology and chemistry. Science 268:1144
-
(1995)
Science
, vol.268
, pp. 1144
-
-
Honig, B.1
Nicholls, A.2
-
60
-
-
0012984110
-
Modelling DNA in aqueous solutions
-
Jayaram B, Aneja N, Rajasekaran E, Arora V, Das A, et al. 1994. Modelling DNA in aqueous solutions. J. Sci. Ind. Res. (India) 53:88
-
(1994)
J. Sci. Ind. Res. (India)
, vol.53
, pp. 88
-
-
Jayaram, B.1
Aneja, N.2
Rajasekaran, E.3
Arora, V.4
Das, A.5
-
61
-
-
0343648651
-
Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: Application to conformational preferences of DNA in aqueous solutions
-
and references therein
-
Jayaram B, Beveridge DL. 1990. Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: application to conformational preferences of DNA in aqueous solutions. J. Phys. Chem. 94:4666 (and references therein)
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 4666
-
-
Jayaram, B.1
Beveridge, D.L.2
-
62
-
-
33751499778
-
Grand canonical Monte Carlo simulations on aqueous solutions of NaCl and NaDNA: Excess chemical potentials and sources of nonideality in electrolyte and polyelectrolyte solutions
-
Jayaram B, Beveridge DL. 1991. Grand canonical Monte Carlo simulations on aqueous solutions of NaCl and NaDNA: excess chemical potentials and sources of nonideality in electrolyte and polyelectrolyte solutions. J. Phys. Chem. 95:2506
-
(1991)
J. Phys. Chem.
, vol.95
, pp. 2506
-
-
Jayaram, B.1
Beveridge, D.L.2
-
63
-
-
1442299978
-
Energetic and kinetic aspects of macromolecular association: A computational study of repressor-operator complexation
-
THEOCHEM. In press
-
Jayaram B, Das A, Aneja N. 1995. Energetic and kinetic aspects of macromolecular association: a computational study of repressor-operator complexation. J. Mol. Struct. (THEOCHEM). In press
-
(1995)
J. Mol. Struct.
-
-
Jayaram, B.1
Das, A.2
Aneja, N.3
-
64
-
-
0001739390
-
A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of λ repressor-operator complex formation
-
Jayaram B, DiCapua FM, Beveridge DL. 1991. A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of λ repressor-operator complex formation. J. Am. Chem. Soc. 113:5211
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 5211
-
-
Jayaram, B.1
DiCapua, F.M.2
Beveridge, D.L.3
-
66
-
-
0025444642
-
Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model
-
Jayaram B, Swaminathan S, Beveridge DL, Sharp K, Honig B. 1990. Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model. Macromolecules 23:3156
-
(1990)
Macromolecules
, vol.23
, pp. 3156
-
-
Jayaram, B.1
Swaminathan, S.2
Beveridge, D.L.3
Sharp, K.4
Honig, B.5
-
67
-
-
0026029516
-
Zinc ion-DNA polymer interactions
-
Jia X, Marzilli LG. 1991. Zinc ion-DNA polymer interactions. Biopolymers 31:23
-
(1991)
Biopolymers
, vol.31
, pp. 23
-
-
Jia, X.1
Marzilli, L.G.2
-
68
-
-
0027435626
-
Comparative spectroscopic, calorimetric and computational studies of nucleic acid complexes with 2′,5″- versus 3′,5″-phosphodiester linkages
-
Jin R, Chapman WH, Srinivasan R, Olson WK, Breslow RD, Breslauer KJ. 1993. Comparative spectroscopic, calorimetric and computational studies of nucleic acid complexes with 2′,5″- versus 3′,5″-phosphodiester linkages. Proc. Natl. Acad. Sci. USA 90:10568
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 10568
-
-
Jin, R.1
Chapman, W.H.2
Srinivasan, R.3
Olson, W.K.4
Breslow, R.D.5
Breslauer, K.J.6
-
70
-
-
0022799313
-
Manganese-deoxyribonucleic acid binding modes: Nuclear magnetic relaxation dispersion results
-
Kennedy SD, Bryant RG. 1986. Manganese-deoxyribonucleic acid binding modes: nuclear magnetic relaxation dispersion results. Biophys. J. 50:669
-
(1986)
Biophys. J.
, vol.50
, pp. 669
-
-
Kennedy, S.D.1
Bryant, R.G.2
-
71
-
-
0025778131
-
Computation of ionic distribution around charged biomolecular structures: Results for right handed and left handed DNA
-
Klement R, Soumpasis DM, Jovin TM. 1991. Computation of ionic distribution around charged biomolecular structures: results for right handed and left handed DNA. Proc. Natl. Acad. Sci. USA 88:4631
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 4631
-
-
Klement, R.1
Soumpasis, D.M.2
Jovin, T.M.3
-
72
-
-
0025264106
-
Inclusion of ionic interactions in force field calculations of charged biomolecules - DNA structural transitions
-
Klement R, Soumpasis DM, Kitzing EV, Jovin TM. 1990. Inclusion of ionic interactions in force field calculations of charged biomolecules - DNA structural transitions. Biopolymers 29:1089
-
(1990)
Biopolymers
, vol.29
, pp. 1089
-
-
Klement, R.1
Soumpasis, D.M.2
Kitzing, E.V.3
Jovin, T.M.4
-
73
-
-
0020856901
-
Calculations of the spatial distribution of charge density in the environment of DNA
-
Klein BJ, Pack GR. 1983. Calculations of the spatial distribution of charge density in the environment of DNA. Biopolymers 22:2331
-
(1983)
Biopolymers
, vol.22
, pp. 2331
-
-
Klein, B.J.1
Pack, G.R.2
-
74
-
-
0024295009
-
Dynamics of repressor-operator recognition: The trilo-encooed tetracycline resistance control
-
Kleinschmidt C, Tovar K, Hillen W, Porschke D. 1988. Dynamics of repressor-operator recognition: the trilo-encooed tetracycline resistance control. Biochemistry 27:1094
-
(1988)
Biochemistry
, vol.27
, pp. 1094
-
-
Kleinschmidt, C.1
Tovar, K.2
Hillen, W.3
Porschke, D.4
-
75
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
Kollman P. 1993. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:2395
-
(1993)
Chem. Rev.
, vol.93
, pp. 2395
-
-
Kollman, P.1
-
76
-
-
0025292904
-
Langevin modes of macromolecules: Application to crambin and DNA hexamers
-
Kottalam J, Case DA. 1990. Langevin modes of macromolecules: application to crambin and DNA hexamers. Biopolymers 29:1409
-
(1990)
Biopolymers
, vol.29
, pp. 1409
-
-
Kottalam, J.1
Case, D.A.2
-
78
-
-
0028128015
-
Monte Carlo and Poisson-Boltzmann calculations of the fraction of counterions bound to DNA
-
Lamm G, Wong L, Pack GR. 1994. Monte Carlo and Poisson-Boltzmann calculations of the fraction of counterions bound to DNA. Biopolymers 34:227
-
(1994)
Biopolymers
, vol.34
, pp. 227
-
-
Lamm, G.1
Wong, L.2
Pack, G.R.3
-
79
-
-
0028261555
-
Modelling DNA conformational mechanics
-
Lavery R, Hartmann B. 1994. Modelling DNA conformational mechanics. Biophys. Chem. 50:33
-
(1994)
Biophys. Chem.
, vol.50
, pp. 33
-
-
Lavery, R.1
Hartmann, B.2
-
80
-
-
0022008114
-
The dependence of the surface electrostatic potential of B-DNA on environmental factors
-
72a. Lavery R, Pullman B. 1985. The dependence of the surface electrostatic potential of B-DNA on environmental factors. J. Biomol. Struct. Dyn. 2: 1021
-
(1985)
J. Biomol. Struct. Dyn.
, vol.2
, pp. 1021
-
-
Lavery, R.1
Pullman, B.2
-
81
-
-
0021383374
-
Monte Carlo determination of the distribution of ions about a cylindrical polyelectrolyte
-
Le Bret M, Zimm BH. 1984. Monte Carlo determination of the distribution of ions about a cylindrical polyelectrolyte. Biopolymers 23:271
-
(1984)
Biopolymers
, vol.23
, pp. 271
-
-
Le Bret, M.1
Zimm, B.H.2
-
82
-
-
0020262664
-
Computer simulation of DNA double helix dynamics
-
Levitt M. 1983. Computer simulation of DNA double helix dynamics. Cold Spring Harbor Symp. Quant. Biol. 47:251
-
(1983)
Cold Spring Harbor Symp. Quant. Biol.
, vol.47
, pp. 251
-
-
Levitt, M.1
-
83
-
-
0022573212
-
Kinetics of protein-nucleic acid interactions: Use of salt effects to prove mechanisms of interaction
-
Lohman TM. 1986. Kinetics of protein-nucleic acid interactions: use of salt effects to prove mechanisms of interaction. CRC Crit. Rev. Biochem. 19:191
-
(1986)
CRC Crit. Rev. Biochem.
, vol.19
, pp. 191
-
-
Lohman, T.M.1
-
84
-
-
0001660190
-
Theoretical studies of DNA during orthogonal field alternating gel electrophoresis
-
Madden TL, Deutsch JM. 1991. Theoretical studies of DNA during orthogonal field alternating gel electrophoresis. J. Chem. Phys. 94:1584
-
(1991)
J. Chem. Phys.
, vol.94
, pp. 1584
-
-
Madden, T.L.1
Deutsch, J.M.2
-
86
-
-
0017895903
-
The molecular theory of polyelectrolyte solutions with application to the electrostatic properties of polynucleotides
-
Manning GS. 1978. The molecular theory of polyelectrolyte solutions with application to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11:179
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 179
-
-
Manning, G.S.1
-
87
-
-
0000541402
-
Counterion binding in polyelectrolyte theory
-
Manning GS. 1979. Counterion binding in polyelectrolyte theory. Acc. Chem. Res. 12:443
-
(1979)
Acc. Chem. Res.
, vol.12
, pp. 443
-
-
Manning, G.S.1
-
88
-
-
0021936282
-
Netropsin binding to poly d(AT)-poly d(AT) and to poly dA-poly dT: A comparative thermodynamic study
-
Marky LA, Curry J, Breslauer KJ. 1985. Netropsin binding to poly d(AT)-poly d(AT) and to poly dA-poly dT: a comparative thermodynamic study. Prog. Clin. Biol. Res. 172:155
-
(1985)
Prog. Clin. Biol. Res.
, vol.172
, pp. 155
-
-
Marky, L.A.1
Curry, J.2
Breslauer, K.J.3
-
89
-
-
0021752280
-
Differential electrostatic stabilization of A, B and Z forms of DNA
-
Matthew JB, Richards FM. 1984. Differential electrostatic stabilization of A, B and Z forms of DNA. Biopolymers 23:2743
-
(1984)
Biopolymers
, vol.23
, pp. 2743
-
-
Matthew, J.B.1
Richards, F.M.2
-
90
-
-
0026253724
-
Distance dependent dielectric constants and their application to double helical DNA
-
Mazur J, Jernigan RL. 1991. Distance dependent dielectric constants and their application to double helical DNA. Biopolymers 31:1615
-
(1991)
Biopolymers
, vol.31
, pp. 1615
-
-
Mazur, J.1
Jernigan, R.L.2
-
93
-
-
0028052906
-
A nanosecond molecular dynamics trajectory for a B DNA double helix: Evidence for substates
-
McConnell KJ, Nirmala R, Young MA, Ravishanker G, Beveridge DL. 1994. A nanosecond molecular dynamics trajectory for a B DNA double helix: evidence for substates. J. Am. Chem. Soc. 116:4461
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 4461
-
-
McConnell, K.J.1
Nirmala, R.2
Young, M.A.3
Ravishanker, G.4
Beveridge, D.L.5
-
94
-
-
0000001012
-
Monte Carlo studies of counterion-DNA interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories
-
Mills P, Anderson CF, Record MT Jr. 1985. Monte Carlo studies of counterion-DNA interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories. J. Phys. Chem. 89:3984
-
(1985)
J. Phys. Chem.
, vol.89
, pp. 3984
-
-
Mills, P.1
Anderson, C.F.2
Record Jr., M.T.3
-
96
-
-
0000883906
-
Grand canonical Monte Carlo calculations of thermodynamic coefficients for a primitive model of DNA-salt solutions
-
Mills P, Anderson CF, Record MT Jr. 1986. Grand canonical Monte Carlo calculations of thermodynamic coefficients for a primitive model of DNA-salt solutions. J. Phys. Chem. 90:6541
-
(1986)
J. Phys. Chem.
, vol.90
, pp. 6541
-
-
Mills, P.1
Anderson, C.F.2
Record Jr., M.T.3
-
98
-
-
0028239626
-
Salt effects on protein-DNA interactions: The lambda cI repressor and Eco RI endonuclease
-
Misra V, Hecht J, Sharp K, Friedman R, Honig B. 1994. Salt effects on protein-DNA interactions: the lambda cI repressor and Eco RI endonuclease. J. Mol. Biol. 238:264
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 264
-
-
Misra, V.1
Hecht, J.2
Sharp, K.3
Friedman, R.4
Honig, B.5
-
99
-
-
0028246710
-
Salt effects on ligand-DNA binding: Minor groove antibiotics
-
Misra V, Sharp K, Friedman R, Honig B. 1994. Salt effects on ligand-DNA binding: minor groove antibiotics. J. Mol. Biol. 238:245
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 245
-
-
Misra, V.1
Sharp, K.2
Friedman, R.3
Honig, B.4
-
100
-
-
0001008705
-
Molecular dynamics simulation of ions and water around triplex DNA
-
Mohan V, Smith PE, Pettitt BM. 1993. Molecular dynamics simulation of ions and water around triplex DNA. J. Phys. Chem. 97:12984
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 12984
-
-
Mohan, V.1
Smith, P.E.2
Pettitt, B.M.3
-
101
-
-
33845378291
-
Ionic distributions near polyelectrolytes. A comparison of theoretical approaches
-
Murthy CS, Bacquet RJ, Rossky PJ. 1985. Ionic distributions near polyelectrolytes. A comparison of theoretical approaches. J. Phys. Chem. 89: 701
-
(1985)
J. Phys. Chem.
, vol.89
, pp. 701
-
-
Murthy, C.S.1
Bacquet, R.J.2
Rossky, P.J.3
-
102
-
-
0026337344
-
Molecular modeling to study DNA intercalation by antitumor drugs in methods in enzymology
-
Neidle S, Jenkins TC. 1991. Molecular modeling to study DNA intercalation by antitumor drugs in methods in enzymology. Methods Enzymol. 203: 433
-
(1991)
Methods Enzymol.
, vol.203
, pp. 433
-
-
Neidle, S.1
Jenkins, T.C.2
-
103
-
-
84988103838
-
Energy functions from energy minimization and dynamics of nucleic acids
-
Nilsson L, Karplus M. 1984. Energy functions from energy minimization and dynamics of nucleic acids. J. Comput. Chem. 1:591
-
(1984)
J. Comput. Chem.
, vol.1
, pp. 591
-
-
Nilsson, L.1
Karplus, M.2
-
104
-
-
0028285106
-
Monte Carlo simulations on potentiometric titration of cylindrical polyelectrolytes: Introduction of a method and its application to model systems without added salt
-
Nishio T. 1994. Monte Carlo simulations on potentiometric titration of cylindrical polyelectrolytes: introduction of a method and its application to model systems without added salt. Biophys. Chem. 49:201
-
(1994)
Biophys. Chem.
, vol.49
, pp. 201
-
-
Nishio, T.1
-
105
-
-
0021760642
-
23Na NMR relaxation study of the effects of conformation and base composition on the interactions of counterions with double-helical DNA
-
23Na NMR relaxation study of the effects of conformation and base composition on the interactions of counterions with double-helical DNA. Biochemistry 23:4309
-
(1984)
Biochemistry
, vol.23
, pp. 4309
-
-
Nordenskiold, L.1
Chang, D.K.2
Anderson, C.F.3
Record Jr., M.T.4
-
106
-
-
0027209697
-
Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves
-
97a. Oberoi H, Allewell N. 1993. Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves. Biophys. J. 65:48
-
(1993)
Biophys. J.
, vol.65
, pp. 48
-
-
Oberoi, H.1
Allewell, N.2
-
107
-
-
0000014960
-
Monte Carlo description of oligoelectrolyte properties of DNA oligomers
-
97b. Olmsted MC, Anderson CF, Record MT. 1989. Monte Carlo description of oligoelectrolyte properties of DNA oligomers. Proc. Natl. Acad. Sci. 86:7766
-
(1989)
Proc. Natl. Acad. Sci.
, vol.86
, pp. 7766
-
-
Olmsted, M.C.1
Anderson, C.F.2
Record, M.T.3
-
108
-
-
0026253640
-
Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysis
-
Olmsted MC, Anderson CF, Record MT 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
-
(1991)
Biopolymers
, vol.31
, pp. 1593
-
-
Olmsted, M.C.1
Anderson, C.F.2
Record Jr., M.T.3
-
109
-
-
0028887796
-
Grand Canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation to the center of DNA oligomers
-
98a. Olmsted MC, Bond J, Anderson CF, Record MT. 1995. Grand Canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation to the center of DNA oligomers. Biophys. J. 68:634
-
(1995)
Biophys. J.
, vol.68
, pp. 634
-
-
Olmsted, M.C.1
Bond, J.2
Anderson, C.F.3
Record, M.T.4
-
110
-
-
8944255827
-
Excess counterion accumulation around branched nucleic acids
-
98b. Olmsted MC, Hagerman PJ. 1995. Excess counterion accumulation around branched nucleic acids. J. Mol. Biol. 238:455
-
(1995)
J. Mol. Biol.
, vol.238
, pp. 455
-
-
Olmsted, M.C.1
Hagerman, P.J.2
-
111
-
-
0026339117
-
Computer simulation of DNA supercoiling
-
Olson WK, Zhang P. 1991. Computer simulation of DNA supercoiling. Methods Enzymol. 203:403
-
(1991)
Methods Enzymol.
, vol.203
, pp. 403
-
-
Olson, W.K.1
Zhang, P.2
-
112
-
-
0001575672
-
A simple theory for thermodynamic properties of polyelectrolyte solutions
-
Oosawa F. 1957. A simple theory for thermodynamic properties of polyelectrolyte solutions. J. Polym. Soc. Jpn. 23:421
-
(1957)
J. Polym. Soc. Jpn.
, vol.23
, pp. 421
-
-
Oosawa, F.1
-
113
-
-
0025086442
-
Molecular mechanics modelling of drug-DNA structures: The effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model
-
Orozco M, Laughton CA, Herzyk P, Neidle S. 1990. Molecular mechanics modelling of drug-DNA structures: the effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model. J. Biomol. Struct. Dyn. 8:359
-
(1990)
J. Biomol. Struct. Dyn.
, vol.8
, pp. 359
-
-
Orozco, M.1
Laughton, C.A.2
Herzyk, P.3
Neidle, S.4
-
114
-
-
0024294634
-
Crystal structure of trp repressor/operator complex at atomic resolution
-
Otwinowsky Z, Schevitz RW, Zhang R-G, Lawson CL, Joachimiak A, et al. 1988. Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335:321
-
(1988)
Nature
, vol.335
, pp. 321
-
-
Otwinowsky, Z.1
Schevitz, R.W.2
Zhang, R.-G.3
Lawson, C.L.4
Joachimiak, A.5
-
115
-
-
84990707598
-
Counterion condensation theory revisited: Limits on its application
-
102a. Pack GR. 1993. Counterion condensation theory revisited: limits on its application. Int. J. Quantum Chem. 20:213-30
-
(1993)
Int. J. Quantum Chem.
, vol.20
, pp. 213-230
-
-
Pack, G.R.1
-
116
-
-
0027379329
-
The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems
-
Pack GR, Garrett GA, Wong L, Lamm G. 1993. The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems. Biophys. J. 65:1363
-
(1993)
Biophys. J.
, vol.65
, pp. 1363
-
-
Pack, G.R.1
Garrett, G.A.2
Wong, L.3
Lamm, G.4
-
118
-
-
0001426265
-
Ion-ion correlations in polyelectrolyte solutions: Hard sphere counterions
-
Penford R, Jonsson B, Nordholm S. 1993. Ion-ion correlations in polyelectrolyte solutions: hard sphere counterions. J. Chem. Phys. 99:497
-
(1993)
J. Chem. Phys.
, vol.99
, pp. 497
-
-
Penford, R.1
Jonsson, B.2
Nordholm, S.3
-
119
-
-
0019598899
-
Molecular electrostatic potential of the nucleic acids
-
Pullman A, Pullman B. 1981. Molecular electrostatic potential of the nucleic acids. Q. Rev. Biophys. 14:289
-
(1981)
Q. Rev. Biophys.
, vol.14
, pp. 289
-
-
Pullman, A.1
Pullman, B.2
-
120
-
-
0020953988
-
Electrostatics of polymorphic DNA
-
Pullman B. 1983. Electrostatics of polymorphic DNA. J. Biomol. Struct. Dyn. 1:773
-
(1983)
J. Biomol. Struct. Dyn.
, vol.1
, pp. 773
-
-
Pullman, B.1
-
121
-
-
0028334940
-
Counterion condensation in DNA systems: The cylindrical Poisson-Boltzmann model revisited
-
Rajasekaran E, Jayaram B. 1994. Counterion condensation in DNA systems: the cylindrical Poisson-Boltzmann model revisited. Biopolymers 34:443
-
(1994)
Biopolymers
, vol.34
, pp. 443
-
-
Rajasekaran, E.1
Jayaram, B.2
-
122
-
-
0000777707
-
Energetic coupling between DNA bending and base-pair opening
-
Ramstein J, Lavery R. 1988. Energetic coupling between DNA bending and base-pair opening. Proc. Natl. Acad. Sci. USA 85:7231
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 7231
-
-
Ramstein, J.1
Lavery, R.2
-
123
-
-
84986522875
-
New method for the computation of ionic distribution of round rod-like polyelectrolytes with the helical distribution of charges. I. General approach and a nonlinearized Poisson-Boltzmann equation
-
Rashin AA, Malinsky J. 1991. New method for the computation of ionic distribution of round rod-like polyelectrolytes with the helical distribution of charges. I. General approach and a nonlinearized Poisson-Boltzmann equation. J. Comp. Chem. 12: 981
-
(1991)
J. Comp. Chem.
, vol.12
, pp. 981
-
-
Rashin, A.A.1
Malinsky, J.2
-
124
-
-
0031516150
-
Treatment of counterions in computer simulations of DNA
-
In press
-
Ravishanker G, Auffinger P, Langley DR, Jayaram B, Young MA, Beveridge DL. 1996. Treatment of counterions in computer simulations of DNA. Rev. Comput. Chem. In press
-
(1996)
Rev. Comput. Chem.
-
-
Ravishanker, G.1
Auffinger, P.2
Langley, D.R.3
Jayaram, B.4
Young, M.A.5
Beveridge, D.L.6
-
126
-
-
0026869974
-
Theory of delocalized ionic binding to polynucleotides: Structural and excluded volume effects
-
112a. Ray J, Manning GS. 1992. Theory of delocalized ionic binding to polynucleotides: structural and excluded volume effects. Biopolymers 32: 541-549
-
(1992)
Biopolymers
, vol.32
, pp. 541-549
-
-
Ray, J.1
Manning, G.S.2
-
127
-
-
0017820499
-
Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The role of ion association and release, screening and ion effects on water activity
-
Record MT Jr, Anderson CF, Lohman T. 1978. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the role of ion association and release, screening and ion effects on water activity. Q. Rev. Biophys. 11:103
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 103
-
-
Record Jr., M.T.1
Anderson, C.F.2
Lohman, T.3
-
128
-
-
0022332472
-
Ions as regulators of protein-nucleic acid interactions in vitro and in vivo
-
Record MT Jr, Anderson CF, Mills P, Mossing M, Roe J-H. 1985. Ions as regulators of protein-nucleic acid interactions in vitro and in vivo. Adv. Biophys. 20:109
-
(1985)
Adv. Biophys.
, vol.20
, pp. 109
-
-
Record Jr., M.T.1
Anderson, C.F.2
Mills, P.3
Mossing, M.4
Roe, J.-H.5
-
129
-
-
2542606126
-
Counterion spin relaxation in DNA solutions: A stochastic dynamics simulation study
-
Reddy MR, Rossky PJ, Murthy CS. 1987. Counterion spin relaxation in DNA solutions: a stochastic dynamics simulation study. J. Phys. Chem. 91:4923
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 4923
-
-
Reddy, M.R.1
Rossky, P.J.2
Murthy, C.S.3
-
130
-
-
0001369897
-
Monte Carlo study of titration of linear polyelectrolyte effects
-
Reed CE, Reed WF. 1991. Monte Carlo study of titration of linear polyelectrolyte effects. J. Chem. Phys. 96: 1609
-
(1991)
J. Chem. Phys.
, vol.96
, pp. 1609
-
-
Reed, C.E.1
Reed, W.F.2
-
131
-
-
0001574661
-
Entropy volume correlation with hydration changes in DNA-ligand interactions
-
Rentzeperis D, Marky LA, Kupke DW. 1992. Entropy volume correlation with hydration changes in DNA-ligand interactions. J. Phys. Chem. 96:9612
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 9612
-
-
Rentzeperis, D.1
Marky, L.A.2
Kupke, D.W.3
-
133
-
-
0000127073
-
Sequence-specific recognition of double helical nucleic acids by proteins
-
Seeman NC, Rosenberg JM, Rich A. 1976. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73:804
-
(1976)
Proc. Natl. Acad. Sci. USA
, vol.73
, pp. 804
-
-
Seeman, N.C.1
Rosenberg, J.M.2
Rich, A.3
-
134
-
-
84965102253
-
-
119a. Seeman NC, Rosenberg JM, Suddath FL, Parkkim JJ, Rich A. 1976. J. Mol. Biol. 104:109
-
(1976)
J. Mol. Biol.
, vol.104
, pp. 109
-
-
Seeman, N.C.1
Rosenberg, J.M.2
Suddath, F.L.3
Parkkim, J.J.4
Rich, A.5
-
135
-
-
0027377079
-
Molecular dynamics investigations of DNA triple helical models: Unique features of the Watson-Crick duplex
-
Sekharudu CY, Yathindra N, Sundaralingam M. 1993. Molecular dynamics investigations of DNA triple helical models: unique features of the Watson-Crick duplex. J. Biomol. Struct. Dyn. 11:225
-
(1993)
J. Biomol. Struct. Dyn.
, vol.11
, pp. 225
-
-
Sekharudu, C.Y.1
Yathindra, N.2
Sundaralingam, M.3
-
136
-
-
0025741694
-
Comparison of operator-specific and nonspecific DNA binding of the λ cI repressor: [KCl] and pH effects
-
Senear DF, Batey R. 1991. Comparison of operator-specific and nonspecific DNA binding of the λ cI repressor: [KCl] and pH effects. Biochemistry 30:6677
-
(1991)
Biochemistry
, vol.30
, pp. 6677
-
-
Senear, D.F.1
Batey, R.2
-
137
-
-
0028215767
-
Electrostatic interactions in macromolecules
-
Sharp K. 1994. Electrostatic interactions in macromolecules. Curr. Opin. Struct. Biol. 4:234
-
(1994)
Curr. Opin. Struct. Biol.
, vol.4
, pp. 234
-
-
Sharp, K.1
-
138
-
-
0029068766
-
Polyelectrolyte electrostatics: Salt dependence, entropic and enthalpic contributions to free energy in the non-linear Poisson-Boltzmann model
-
In press
-
122a. Sharp K. 1995. Polyelectrolyte electrostatics: salt dependence, entropic and enthalpic contributions to free energy in the non-linear Poisson-Boltzmann model. Biopolymers. In press
-
(1995)
Biopolymers.
-
-
Sharp, K.1
-
139
-
-
0029038105
-
Salt effects on polyelectrolyte-ligand binding: Comparison of Poisson Boltzmann and limiting law counterion binding models
-
In press
-
122b. Sharp K, Friedman R, Misra V, Hecht J, Honig B. 1995. Salt effects on polyelectrolyte-ligand binding: comparison of Poisson Boltzmann and limiting law counterion binding models. Biopolymers. In press
-
(1995)
Biopolymers
-
-
Sharp, K.1
Friedman, R.2
Misra, V.3
Hecht, J.4
Honig, B.5
-
140
-
-
0025283002
-
Electrostatic interactions in macromolecules: Theory and applications
-
Sharp K, Honig B. 1990. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:301
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 301
-
-
Sharp, K.1
Honig, B.2
-
142
-
-
0001555216
-
A molecular dynamics simulation of double helical B-DNA including counterions and water
-
Siebel GL, Singh UC, Kollman PA. 1985. A molecular dynamics simulation of double helical B-DNA including counterions and water. Proc. Natl. Acad. Sci. USA 82:6537
-
(1985)
Proc. Natl. Acad. Sci. USA
, vol.82
, pp. 6537
-
-
Siebel, G.L.1
Singh, U.C.2
Kollman, P.A.3
-
143
-
-
0007158350
-
Contributions of the polyion and counterions to the internal and free energies of polyelectrolyte solutions
-
Skerjanc J. 1990. Contributions of the polyion and counterions to the internal and free energies of polyelectrolyte solutions. J. Chem. Phys. 93: 6731
-
(1990)
J. Chem. Phys.
, vol.93
, pp. 6731
-
-
Skerjanc, J.1
-
144
-
-
0026253887
-
+ on the persistence length and excluded volume of T7 bacteriophage DNA
-
+ on the persistence length and excluded volume of T7 bacteriophage DNA. Biopolymers 31:1559
-
(1991)
Biopolymers
, vol.31
, pp. 1559
-
-
Sobel, E.S.1
Harpst, J.A.2
-
145
-
-
0007646582
-
Statistical mechanics of the B-Z transition of DNA: Contribution of diffuse ionic interactions
-
Soumpasis DM. 1984. Statistical mechanics of the B-Z transition of DNA: contribution of diffuse ionic interactions. Proc. Natl. Acad. Sci. USA 81:5116
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 5116
-
-
Soumpasis, D.M.1
-
146
-
-
0001370674
-
Theory for second virial coefficients of short DNA
-
Stigter D, Dill KA. 1993. Theory for second virial coefficients of short DNA. J. Phys. Chem. 97:12995
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 12995
-
-
Stigter, D.1
Dill, K.A.2
-
147
-
-
0024121512
-
Theoretical considerations on the "spine of hydration" in the minor groove of d(CGC GA at TCG CG) d (GC GC T-TAAGCGC): Monte Carlo computer simulations
-
Subramanian P, Ravishanker G, Beveridge DL. 1988. Theoretical considerations on the "spine of hydration" in the minor groove of d(CGC GA AT TCG CG) d (GC GC T-TAAGCGC): Monte Carlo computer simulations. Proc. Natl. Acad. Sci. USA 85:1836
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 1836
-
-
Subramanian, P.1
Ravishanker, G.2
Beveridge, D.L.3
-
148
-
-
0006613264
-
Molecular dynamics simulation of a deoxynucleoside-drug intercalation complex: DCpG/ proflayin
-
Swaminathan S, Beveridge DL, Berman HM. 1990. Molecular dynamics simulation of a deoxynucleoside-drug intercalation complex: dCpG/ proflayin. J. Phys. Chem. 94:4660
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 4660
-
-
Swaminathan, S.1
Beveridge, D.L.2
Berman, H.M.3
-
149
-
-
0000930430
-
Molecular dynamics of B-DNA including counterions and water: A 140 psec trajectory for d(CGCGAATTCGCG) based on the GROMOS force field
-
Swaminathan S, Ravishanker G, Beveridge DL. 1991. Molecular dynamics of B-DNA including counterions and water: a 140 psec trajectory for d(CGCGAATTCGCG) based on the GROMOS force field. J. Am. Chem. Soc. 113:5027
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 5027
-
-
Swaminathan, S.1
Ravishanker, G.2
Beveridge, D.L.3
-
150
-
-
0023449766
-
Hydration structure and dynamics of B-and Z-DNA in the presence of counterions via molecular dynamics simulations
-
Swamy KN, Clementi E. 1987. Hydration structure and dynamics of B-and Z-DNA in the presence of counterions via molecular dynamics simulations. Biopolymers 26:1901
-
(1987)
Biopolymers
, vol.26
, pp. 1901
-
-
Swamy, K.N.1
Clementi, E.2
-
151
-
-
0025355712
-
Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl dependence of DNA flexibility and helical repeat
-
Taylor WH, Hagerman PJ. 1990. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212:363
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 363
-
-
Taylor, W.H.1
Hagerman, P.J.2
-
152
-
-
11744256643
-
Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
-
Tomasi J, Persico M. 1994. Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem. Rev. 94:2027
-
(1994)
Chem. Rev.
, vol.94
, pp. 2027
-
-
Tomasi, J.1
Persico, M.2
-
153
-
-
33845376356
-
Electrostatic effects on ion distribution around aqueous macromolecules
-
Troll MT, Roitman D, Conrad J, Zimm BH. 1986. Electrostatic effects on ion distribution around aqueous macromolecules. Macromolecules 19:1186
-
(1986)
Macromolecules
, vol.19
, pp. 1186
-
-
Troll, M.T.1
Roitman, D.2
Conrad, J.3
Zimm, B.H.4
-
155
-
-
0001449615
-
Flexible polyelectrolyte in ionic solution: A Monte Carlo study
-
Valleau JP. 1989. Flexible polyelectrolyte in ionic solution: a Monte Carlo study. Chem. Phys. 129:163
-
(1989)
Chem. Phys.
, vol.129
, pp. 163
-
-
Valleau, J.P.1
-
156
-
-
2142813682
-
Computer simulation of molecular dynamics: Methodology, applications and perspectives in chemistry
-
van Gunsteren WF, Berendsen HJC. 1990. Computer simulation of molecular dynamics: methodology, applications and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 29: 992
-
(1990)
Angew. Chem. Int. Ed. Engl.
, vol.29
, pp. 992
-
-
Gunsteren, W.F.1
Berendsen, H.J.C.2
-
157
-
-
36549096819
-
A grand canonical Monte Carlo simulation study of polyelectrolyte solutions
-
Vlachy V, Haymet ADJ. 1986. A grand canonical Monte Carlo simulation study of polyelectrolyte solutions. J. Chem. Phys. 84:5874
-
(1986)
J. Chem. Phys.
, vol.84
, pp. 5874
-
-
Vlachy, V.1
Haymet, A.D.J.2
-
159
-
-
0026713204
-
Modeling DNA structures: Molecular mechanics and molecular dynamics
-
von Kitzing E. 1992. Modeling DNA structures: molecular mechanics and molecular dynamics. Methods Enzymol. 211:449
-
(1992)
Methods Enzymol.
, vol.211
, pp. 449
-
-
Kitzing, E.1
-
162
-
-
0026511587
-
Towards a dynamical structure of duplex DNA in solution: Comparison of theoretical and experimental NOE intensities of d(CGCGAATTCGCG)
-
Whitka JM, Swaminathan S, Srinivasan J, Beveridge DL, Bolton PH. 1992. Towards a dynamical structure of duplex DNA in solution: comparison of theoretical and experimental NOE intensities of d(CGCGAATTCGCG). Science 255:597
-
(1992)
Science
, vol.255
, pp. 597
-
-
Whitka, J.M.1
Swaminathan, S.2
Srinivasan, J.3
Beveridge, D.L.4
Bolton, P.H.5
-
163
-
-
0024328777
-
Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC
-
Williams AP, Longfellow CE, Freier SM, Kierzek R, Turner DH. 1989. Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry 28:4283
-
(1989)
Biochemistry
, vol.28
, pp. 4283
-
-
Williams, A.P.1
Longfellow, C.E.2
Freier, S.M.3
Kierzek, R.4
Turner, D.H.5
-
164
-
-
0019887628
-
Diffusion driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interactions: Kinetic measurements and conclusions
-
Winter RB, Berg OG, von Hippel PH. 1981. Diffusion driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interactions: kinetic measurements and conclusions. Biochemistry 20:6929
-
(1981)
Biochemistry
, vol.20
, pp. 6929
-
-
Winter, R.B.1
Berg, O.G.2
Von Hippel, P.H.3
-
165
-
-
8944229901
-
Counterions may intrude into the spine of hydration in the minor groove of the B DNA double helix: The "AT pocket."
-
Submitted
-
146a. Young M, Jayaram B, Beveridge DL. 1996. Counterions may intrude into the spine of hydration in the minor groove of the B DNA double helix: the "AT pocket." J. Am. Chem. Soc. Submitted
-
(1996)
J. Am. Chem. Soc.
-
-
Young, M.1
Jayaram, B.2
Beveridge, D.L.3
-
166
-
-
8944240556
-
Nanosecond molecular dynamics trajectories for a B DNA oligonucleotide and explicit water and counterions based on the AMBER force field
-
Submitted
-
146b. Young MA, Ravishanker G, Beveridge DL. 1996. Nanosecond molecular dynamics trajectories for a B DNA oligonucleotide and explicit water and counterions based on the AMBER force field. Biophys. J. Submitted
-
(1996)
Biophys. J.
-
-
Young, M.A.1
Ravishanker, G.2
Beveridge, D.L.3
-
167
-
-
0029110156
-
Toward the accurate modeling of DNA: The importance of long-range electrostatics
-
York DM, Yang W, Lee H, Darden T, Pedersen LG. 1995. Toward the accurate modeling of DNA: the importance of long-range electrostatics. J. Am. Chem. Soc. 117:5001
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5001
-
-
York, D.M.1
Yang, W.2
Lee, H.3
Darden, T.4
Pedersen, L.G.5
-
168
-
-
0026619551
-
Poisson-Boltzmann analysis of the lambda repressor-operator interaction
-
Zacharias M, Luty BA, Davis ME, McCammon JA. 1992. Poisson-Boltzmann analysis of the lambda repressor-operator interaction. Biophys. J. 63:1280
-
(1992)
Biophys. J.
, vol.63
, pp. 1280
-
-
Zacharias, M.1
Luty, B.A.2
Davis, M.E.3
McCammon, J.A.4
-
170
-
-
36449007981
-
Lakes-straits model of field inversion gel electrophoresis of DNA
-
Zimm BH. 1991. Lakes-straits model of field inversion gel electrophoresis of DNA. J. Chem. Phys. 94:2187
-
(1991)
J. Chem. Phys.
, vol.94
, pp. 2187
-
-
Zimm, B.H.1
-
171
-
-
0020954109
-
Counterion condensation and system dimensionality
-
Zimm BH, LeBret M. 1983. Counterion condensation and system dimensionality. J. Biomol. Struct. Dyn. 1: 461
-
(1983)
J. Biomol. Struct. Dyn.
, vol.1
, pp. 461
-
-
Zimm, B.H.1
LeBret, M.2
|