-
1
-
-
0026742978
-
The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids
-
H. M. Berman, W. K. Olson, D. L. Beveridge, J. Westbrook, A. Gelbin, T. Demeny, S. H. Hsieh, and A. R. Srinivasan, Biophys. J., 63, 751 (1992). The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. See Web site at Rutgers University, http://ndbserver.rutgers.edu/.
-
(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
Demeny, T.6
Hsieh, S.H.7
Srinivasan, A.R.8
-
2
-
-
0017411710
-
The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures
-
F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, J. Mol. Biol., 112, 535 (1977). The Protein Data Bank: A Computer-Based Archival File for Macromolecular Structures.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer E.F., Jr.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
3
-
-
0002593973
-
Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Olipomers
-
E. Westhof, Ed., CRC Press, Boca Raton, FL
-
D. L. Beveridge, S. Swaminathan, G. Ravishanker, J. M. Withka, J. Srinivasan, C. Prevost, S. Louise-May, D. R. Langley, F. M. DiCapua, and P. H. Bolton, in Water and Biological Macromolecules, E. Westhof, Ed., CRC Press, Boca Raton, FL, 1993, pp. 165-225. Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Olipomers.
-
(1993)
Water and Biological Macromolecules
, pp. 165-225
-
-
Beveridge, D.L.1
Swaminathan, S.2
Ravishanker, G.3
Withka, J.M.4
Srinivasan, J.5
Prevost, C.6
Louise-May, S.7
Langley, D.R.8
DiCapua, F.M.9
Bolton, P.H.10
-
5
-
-
0001227508
-
Methods for the Evaluation of Long-Range Electrostatic Forces in Computer Simulations of Molecular Systems
-
W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Eds., ESCOM, Leiden
-
P. E. Smith and W. F. van Gunsteren, in Computer Simulation of Biomolecular Systems, W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Eds., ESCOM, Leiden, 1993, pp. 182-211. Methods for the Evaluation of Long-Range Electrostatic Forces in Computer Simulations of Molecular Systems.
-
(1993)
Computer Simulation of Biomolecular Systems
, pp. 182-211
-
-
Smith, P.E.1
Van Gunsteren, W.F.2
-
6
-
-
0042543436
-
Electrostatic-Interactions
-
W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Eds., ESCOM, Leiden
-
H.J.C. Berendsen, in Computer Simulation of Biomolecular Systems, W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, Eds., ESCOM, Leiden, 1993, pp. 161-181. Electrostatic-Interactions.
-
(1993)
Computer Simulation of Biomolecular Systems
, pp. 161-181
-
-
Berendsen, H.J.C.1
-
8
-
-
0009663089
-
What Do We Really Know about B-DNA?
-
R. H. Sarma and M. H. Sarma, Eds., Adenine Press, New York
-
R. E. Dickerson, in Structure & Methods, Vol. 3: DNA & RNA, R. H. Sarma and M. H. Sarma, Eds., Adenine Press, New York, 1990, pp. 1-38. What Do We Really Know About B-DNA?
-
(1990)
Structure & Methods, Vol. 3: DNA & RNA
, vol.3
, pp. 1-38
-
-
Dickerson, R.E.1
-
9
-
-
0026702486
-
DNA Structure from A to Z
-
R. E. Dickerson, Methods Enzymol., 211, 67 (1991). DNA Structure from A to Z.
-
(1991)
Methods Enzymol.
, vol.211
, pp. 67
-
-
Dickerson, R.E.1
-
10
-
-
0015749250
-
Refinement of the Structure of B-DNA and Implications for the Analysis of X-Ray Diffraction Data from Fibres of Biopolymers
-
S. Arnott and D. W. L. Hukins, J. Mol. Biol., 81, 93 (1973). Refinement of the Structure of B-DNA and Implications for the Analysis of X-Ray Diffraction Data from Fibres of Biopolymers.
-
(1973)
J. Mol. Biol.
, vol.81
, pp. 93
-
-
Arnott, S.1
Hukins, D.W.L.2
-
11
-
-
0000946971
-
Atomic Coordinates and Molecular Conformations for DNA-DNA, RNA-RNA, and DNA-RNA Helices
-
G. Fasman, Ed., CRC Press, Cleveland, Third edition, Nucleic Acids
-
S. Arnott, P. J. Campbell Smith, and R. Chandrasekaran, in CRC Handbook of Biochemistry and Molecular Biology, G. Fasman, Ed., CRC Press, Cleveland, 1976, Third edition, Nucleic Acids-Vol.II, pp. 411-422. Atomic Coordinates and Molecular Conformations for DNA-DNA, RNA-RNA, and DNA-RNA Helices.
-
(1976)
CRC Handbook of Biochemistry and Molecular Biology
, vol.2
, pp. 411-422
-
-
Arnott, S.1
Campbell Smith, P.J.2
Chandrasekaran, R.3
-
12
-
-
0018866122
-
Left-Handed DNA Helices
-
S. Arnott, R. Chandrasekaran, D. L. Birdsall, A. G. W. Leslie, and R. L. Ratliffe, Nature, 283, 743 (1980). Left-Handed DNA Helices.
-
(1980)
Nature
, vol.283
, pp. 743
-
-
Arnott, S.1
Chandrasekaran, R.2
Birdsall, D.L.3
Leslie, A.G.W.4
Ratliffe, R.L.5
-
13
-
-
0346660091
-
X-ray Fibre Diffraction Studies of DNA: Recent Results and Future Possibilities
-
S. Neidle and E. Westhof, Eds., Macmillan Press, London
-
W. Fuller and A. Mahendrasingam, in Nucleic Acid Structure, S. Neidle and E. Westhof, Eds., Macmillan Press, London, 1987, pp. 101-131. X-ray Fibre Diffraction Studies of DNA: Recent Results and Future Possibilities.
-
(1987)
Nucleic Acid Structure
, pp. 101-131
-
-
Fuller, W.1
Mahendrasingam, A.2
-
14
-
-
0017895903
-
The Molecular Theory of Polyelectrolyte Solutions with Applications to the Electrostatic Properties of Polynucleotides
-
G. S. Manning, Q. Rev. Biophys., 11, 179 (1978). The Molecular Theory of Polyelectrolyte Solutions with Applications to the Electrostatic Properties of Polynucleotides.
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 179
-
-
Manning, G.S.1
-
15
-
-
0000767958
-
Relative Binding Affinities of Monovalent Cations for Double-Stranded DNA Studied by Sodium-23 NMR
-
M. L. Bleam, C. F. Anderson, and M. T. Record Jr., Proc. Natl. Acad. Sci. USA, 77, 3085 (1980). Relative Binding Affinities of Monovalent Cations for Double-Stranded DNA Studied by Sodium-23 NMR.
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 3085
-
-
Bleam, M.L.1
Anderson, C.F.2
Record M.T., Jr.3
-
16
-
-
0020954109
-
Counterion Condensation and System Dimensionality
-
B. H. Zimm and M. Le Bret, J. Biomol. Struct. Dyn., 1, 461 (1983). Counterion Condensation and System Dimensionality.
-
(1983)
J. Biomol. Struct. Dyn.
, vol.1
, pp. 461
-
-
Zimm, B.H.1
Le Bret, M.2
-
17
-
-
2542606126
-
Counterion Spin Relaxation in DNA Solutions: A Stochastic Dynamics Simulation Study
-
M. R. Reddy, P. J. Rossky, and C. S. Murthy, J. Phys. Chem., 91, 4923 (1987). Counterion Spin Relaxation in DNA Solutions: A Stochastic Dynamics Simulation Study.
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 4923
-
-
Reddy, M.R.1
Rossky, P.J.2
Murthy, C.S.3
-
18
-
-
0025444642
-
Monte Carlo Simulation Studies on the Structure of the Counterion Atmosphere of B-DNA. Variations on the Primitive Dielectric Model
-
B. Jayaram, S. Swaminathan, D. L. Beveridge, K. Sharp, and B. Honig, Macromolecules, 23, 3156 (1990). Monte Carlo Simulation Studies on the Structure of the Counterion Atmosphere of B-DNA. Variations on the Primitive Dielectric Model.
-
(1990)
Macromolecules
, vol.23
, pp. 3156
-
-
Jayaram, B.1
Swaminathan, S.2
Beveridge, D.L.3
Sharp, K.4
Honig, B.5
-
19
-
-
0023085903
-
Nuclear Magnetic Resonance and Distance Geometry Studies of DNA Structures in Solution
-
D. J. Patel and L. Shapiro, Annu. Rev. Biophys. Biophys. Chem., 16, 423 (1987). Nuclear Magnetic Resonance and Distance Geometry Studies of DNA Structures in Solution.
-
(1987)
Annu. Rev. Biophys. Biophys. Chem.
, vol.16
, pp. 423
-
-
Patel, D.J.1
Shapiro, L.2
-
20
-
-
84988109709
-
Nucleic Acids and Nuclear Magnetic Resonance
-
J. M. Van de Ven and C. W. Hilbers, Eur. J. Biochem., 178, 1 (1988). Nucleic Acids and Nuclear Magnetic Resonance.
-
(1988)
Eur. J. Biochem.
, vol.178
, pp. 1
-
-
Van De Ven, J.M.1
Hilbers, C.W.2
-
21
-
-
0001262285
-
The Applicability of NMR Methods to the Solution Structure of Nucleic Acids
-
D. E. Wemmer, Curr. Opin. Struct. Biol., 1, 452 (1991). The Applicability of NMR Methods to the Solution Structure of Nucleic Acids.
-
(1991)
Curr. Opin. Struct. Biol.
, vol.1
, pp. 452
-
-
Wemmer, D.E.1
-
22
-
-
0028005009
-
Statistical Analysis of DNA Duplex Structures in Solution Derived by High Resolution NMR
-
N. B. Ulyanov and T. L. James, Appl. Magn. Resonance, 7, 21 (1994). Statistical Analysis of DNA Duplex Structures in Solution Derived by High Resolution NMR.
-
(1994)
Appl. Magn. Resonance
, vol.7
, pp. 21
-
-
Ulyanov, N.B.1
James, T.L.2
-
23
-
-
2142813682
-
Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry
-
W. F. van Gunsteren and H. J. C. Berendsen, Angew. Chem., Int. Ed. Engl., 29, 992 (1990). Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry.
-
(1990)
Angew. Chem., Int. Ed. Engl.
, vol.29
, pp. 992
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
25
-
-
0038497542
-
A Structure for Deoxyribonucleic Acid
-
J. D. Watson and F. H. C. Crick, Nature, 171, 737 (1953). A Structure for Deoxyribonucleic Acid.
-
(1953)
Nature
, vol.171
, pp. 737
-
-
Watson, J.D.1
Crick, F.H.C.2
-
26
-
-
0019326076
-
Polymorphism of DNA Double Helices
-
A. G. W. Leslie, S. Arnott, R. Chandrasekaran, and R. L. Ratliff, J. Mol. Biol., 143, 49 (1980). Polymorphism of DNA Double Helices.
-
(1980)
J. Mol. Biol.
, vol.143
, pp. 49
-
-
Leslie, A.G.W.1
Arnott, S.2
Chandrasekaran, R.3
Ratliff, R.L.4
-
27
-
-
0041936278
-
The Development of Versions 3 and 4 of the Cambridge Structural Database System
-
F. H. Allen, J. E. Davies, J. J. Galloy, O. Johnson, O. Kennard, C. F. Macrae, E. M. Mitchell, G. F. Mitchell, J. M. Smith, and D. G. Watson, J. Chem. Inf. Comput. Sci., 31, 187 (1991). The Development of Versions 3 and 4 of the Cambridge Structural Database System.
-
(1991)
J. Chem. Inf. Comput. Sci.
, vol.31
, pp. 187
-
-
Allen, F.H.1
Davies, J.E.2
Galloy, J.J.3
Johnson, O.4
Kennard, O.5
Macrae, C.F.6
Mitchell, E.M.7
Mitchell, G.F.8
Smith, J.M.9
Watson, D.G.10
-
28
-
-
0042660614
-
Molecular Structure of a Left-Handed Double Helical DNA Fragment at Atomic Resolution
-
A. H. J. Wang, G. J. Quigley, F. J. Kolpak, J. L. Crawford, J. H. van Boom, G. van der Marel, and A. Rich, Nature, 283, 743 (1979). Molecular Structure of a Left-Handed Double Helical DNA Fragment at Atomic Resolution.
-
(1979)
Nature
, vol.283
, pp. 743
-
-
Wang, A.H.J.1
Quigley, G.J.2
Kolpak, F.J.3
Crawford, J.L.4
Van Boom, J.H.5
Van Der Marel, G.6
Rich, A.7
-
29
-
-
0019387686
-
Structure of a B DNA Dodecamer. II. Influence of Base Sequence on Helix Structure
-
R. E. Dickerson and H. R. Drew, J. Mol. Biol., 149, 761 (1981). Structure of a B DNA Dodecamer. II. Influence of Base Sequence on Helix Structure.
-
(1981)
J. Mol. Biol.
, vol.149
, pp. 761
-
-
Dickerson, R.E.1
Drew, H.R.2
-
30
-
-
0024454946
-
Definitions and Nomenclature of Nucleic Acid Structure Parameters
-
R. E. Dickerson, M. Bansal, C. R. Calladine, S. Diekmann, W. N. Hunter, O. Kennard, E. von Kitzing, R. Lavery, H. C. M. Nelson, W. K. Olson, W. Saenger, Z. Shakked, H. Sklenar, D. M. Soumpasis, C. S. Tung, A. H. J. Wang, and V. B. Zhurkin, EMBO J., 8, 1 (1989). Definitions and Nomenclature of Nucleic Acid Structure Parameters.
-
(1989)
EMBO J.
, vol.8
, pp. 1
-
-
Dickerson, R.E.1
Bansal, M.2
Calladine, C.R.3
Diekmann, S.4
Hunter, W.N.5
Kennard, O.6
Von Kitzing, E.7
Lavery, R.8
Nelson, H.C.M.9
Olson, W.K.10
Saenger, W.11
Shakked, Z.12
Sklenar, H.13
Soumpasis, D.M.14
Tung, C.S.15
Wang, A.H.J.16
Zhurkin, V.B.17
-
31
-
-
0028230287
-
Nucleic Acid Structure Analysis. Mathematics for Local Cartesian and Helical Structure Parameters That Are Truly Comparable between Structures
-
M. S. Babcock, E. P. D. Pendault, and W. K. Olson, J. Mol. Biol., 237, 125 (1994). Nucleic Acid Structure Analysis. Mathematics for Local Cartesian and Helical Structure Parameters That Are Truly Comparable Between Structures.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 125
-
-
Babcock, M.S.1
Pendault, E.P.D.2
Olson, W.K.3
-
32
-
-
0011064733
-
-
Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA
-
R. E. Dickerson, Newhelix, Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA.
-
Newhelix
-
-
Dickerson, R.E.1
-
33
-
-
0024539180
-
Defining the Structure of Irregular Nucleic Acids: Conventions and Principles
-
R. Lavery and H. Sklenar, J. Biomol. Struct. Dyn., 6, 655 (1989). Defining the Structure of Irregular Nucleic Acids: Conventions and Principles.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 655
-
-
Lavery, R.1
Sklenar, H.2
-
34
-
-
0026698647
-
Groove Width and Depth of B-DNA Structures Depend on Local Variation in Slide
-
D. Bhattacharyya and M. Bansal, J. Biomol. Struct. Dyn., 10, 213 (1992). Groove Width and Depth of B-DNA Structures Depend on Local Variation in Slide.
-
(1992)
J. Biomol. Struct. Dyn.
, vol.10
, pp. 213
-
-
Bhattacharyya, D.1
Bansal, M.2
-
35
-
-
0027560145
-
Looking into the Grooves of DNA
-
N. Boutonnet, X. Hui, and K. Zakrzewska, Biopolymers, 33, 479 (1993). Looking into the Grooves of DNA.
-
(1993)
Biopolymers
, vol.33
, pp. 479
-
-
Boutonnet, N.1
Hui, X.2
Zakrzewska, K.3
-
36
-
-
0028184697
-
Measuring the Geometry of DNA Grooves
-
E. Stofer and R. Lavery, Biopolymers, 34, 337 (1994). Measuring the Geometry of DNA Grooves.
-
(1994)
Biopolymers
, vol.34
, pp. 337
-
-
Stofer, E.1
Lavery, R.2
-
37
-
-
0001063425
-
Junction and Bends in Nucleic Acids: A New Theoretical Modelling Approach
-
W. K. Olson, M. H. Sarma, R. H. Sarma, and M. Sundaralingam, Eds., Adenine Press, Schenectady, New York
-
R. Lavery, in Structure and Expression, Vol. 3, DNA Bending and Curvature, W. K. Olson, M. H. Sarma, R. H. Sarma, and M. Sundaralingam, Eds., Adenine Press, Schenectady, New York, 1988, pp. 191-211. Junction and Bends in Nucleic Acids: A New Theoretical Modelling Approach.
-
(1988)
Structure and Expression, Vol. 3, DNA Bending and Curvature
, vol.3
, pp. 191-211
-
-
Lavery, R.1
-
38
-
-
0029006896
-
Analysis of Local Helix Bending in Crystal Structures of DNA Oligonucleotides and DNA-Protein Complexes
-
M. A. Young, G. Ravishanker, D. L. Beveridge, and H. M. Berman, Biophys. J., 68, 2452 (1995). Analysis of Local Helix Bending in Crystal Structures of DNA Oligonucleotides and DNA-Protein Complexes.
-
(1995)
Biophys. J.
, vol.68
, pp. 2452
-
-
Young, M.A.1
Ravishanker, G.2
Beveridge, D.L.3
Berman, H.M.4
-
39
-
-
0023042016
-
Structure Refinement of Oligonucleotides by Molecular Dynamics with Nuclear Overhauser Effect Interproton Distance Restraints: Application to 5′ d(CGTACG)
-
L. Nilsson, G. M. Clore, A. M. Gronenborn, A. T. Brunger, and M. Karplus, J. Mol. Biol., 188, 455 (1986). Structure Refinement of Oligonucleotides by Molecular Dynamics with Nuclear Overhauser Effect Interproton Distance Restraints: Application to 5′ d(CGTACG).
-
(1986)
J. Mol. Biol.
, vol.188
, pp. 455
-
-
Nilsson, L.1
Clore, G.M.2
Gronenborn, A.M.3
Brunger, A.T.4
Karplus, M.5
-
40
-
-
0000299865
-
A New Method for Refinement of Macromolecular Structures Based on Nuclear Overhauser Spectra
-
P. Yip and D. A. Case, J. Magn. Res., 83, 643 (1989). A New Method for Refinement of Macromolecular Structures Based on Nuclear Overhauser Spectra.
-
(1989)
J. Magn. Res.
, vol.83
, pp. 643
-
-
Yip, P.1
Case, D.A.2
-
41
-
-
85050563277
-
Molecular Modeling Using Nuclear Magnetic Resonance Data
-
K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York
-
A. E. Torda and W. F. van Gunsteren, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, Vol. 3, pp. 143-172. Molecular Modeling Using Nuclear Magnetic Resonance Data.
-
Reviews in Computational Chemistry
, vol.3
, pp. 143-172
-
-
Torda, A.E.1
Van Gunsteren, W.F.2
-
42
-
-
11644276439
-
Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions. 1. Colligative Properties
-
G. S. Manning, J. Chem. Phys., 51, 924 (1969). Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions. 1. Colligative Properties.
-
(1969)
J. Chem. Phys.
, vol.51
, pp. 924
-
-
Manning, G.S.1
-
44
-
-
0017836325
-
Sodium-23 NMR Studies of Cation-DNA Interactions
-
C. F. Anderson, M. T. Record Jr., and P. A. Hart, Biophys. Chem., 7, 301 (1978). Sodium-23 NMR Studies of Cation-DNA Interactions.
-
(1978)
Biophys. Chem.
, vol.7
, pp. 301
-
-
Anderson, C.F.1
Record M.T., Jr.2
Hart, P.A.3
-
45
-
-
0000806644
-
Sodium-23 Nuclear Magnetic Resonance Studies of Cation-DNA Interactions
-
M. L. Bleam, C. F. Anderson, and M. T. Record Jr., Biochemistry, 22, 5418 (1983). Sodium-23 Nuclear Magnetic Resonance Studies of Cation-DNA Interactions.
-
(1983)
Biochemistry
, vol.22
, pp. 5418
-
-
Bleam, M.L.1
Anderson, C.F.2
Record M.T., Jr.3
-
46
-
-
0023912783
-
Interaction of an N-Methylated Polyamine Analogue, Hexamethonium (2+), with NaDNA: Quantitative N-14 and Na-23 NMR Relaxation Rate Studies of the Cation-Exchange Process
-
S. Padmanabhan, B. Richey, C. F. Anderson, and M. T. Record Jr., Biochemistry, 27, 4367 (1988). Interaction of an N-Methylated Polyamine Analogue, Hexamethonium (2+), with NaDNA: Quantitative N-14 and Na-23 NMR Relaxation Rate Studies of the Cation-Exchange Process.
-
(1988)
Biochemistry
, vol.27
, pp. 4367
-
-
Padmanabhan, S.1
Richey, B.2
Anderson, C.F.3
Record M.T., Jr.4
-
47
-
-
0024519056
-
An Estimate of the Extent of Folding of Nucleosomal DNA by Laterally Asymmetric Neutralization of the Phosphate Groups
-
G. S. Manning, K. K. Ebralidse, A. D. Mirzabekov, and A. Rich, J. Biomol. Struct. Dyn., 6, 877 (1989). An Estimate of the Extent of Folding of Nucleosomal DNA by Laterally Asymmetric Neutralization of the Phosphate Groups.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 877
-
-
Manning, G.S.1
Ebralidse, K.K.2
Mirzabekov, A.D.3
Rich, A.4
-
48
-
-
0025672928
-
Approach to the Limit of Counterion Condensation
-
M. O. Fenley, G. S. Manning, and W. K. Olson, Biopolymers, 30, 1191 (1990). Approach to the Limit of Counterion Condensation.
-
(1990)
Biopolymers
, vol.30
, pp. 1191
-
-
Fenley, M.O.1
Manning, G.S.2
Olson, W.K.3
-
49
-
-
0025335714
-
A Ligand Binding Model of Counterion Condensation to Finite Length Polyelectrolytes
-
T. G. Dewey, Biopolymers, 29, 1793 (1990). A Ligand Binding Model of Counterion Condensation to Finite Length Polyelectrolytes.
-
(1990)
Biopolymers
, vol.29
, pp. 1793
-
-
Dewey, T.G.1
-
50
-
-
0343648651
-
Free Energy of an Arbitrary Charge Distribution Imbedded in Coaxial Cylindrical Dielectric Continua: Application to Conformational Preferences of DNA in Aqueous Solution
-
B. Jayaram and D. L. Beveridge, J. Phys. Chem., 94, 4666 (1990). Free Energy of an Arbitrary Charge Distribution Imbedded in Coaxial Cylindrical Dielectric Continua: Application to Conformational Preferences of DNA in Aqueous Solution.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 4666
-
-
Jayaram, B.1
Beveridge, D.L.2
-
51
-
-
0347920632
-
Molecular Electrostatic Potential Versus Field. Significance for DNA and Its Constituents
-
A. Pullman, B. Pullman, and R. Lavery, J. Mol. Struct., 93, 85 (1983). Molecular Electrostatic Potential Versus Field. Significance for DNA and Its Constituents.
-
(1983)
J. Mol. Struct.
, vol.93
, pp. 85
-
-
Pullman, A.1
Pullman, B.2
Lavery, R.3
-
52
-
-
0343757149
-
Harmonic-Vibrations and Thermodynamic Stability of a DNA Oligomer in Monovalent Salt Solution
-
A. E. Garcia and D. M. Soumpasis, Proc. Natl. Acad. Sci. USA, 86, 3160 (1989). Harmonic-Vibrations and Thermodynamic Stability of a DNA Oligomer in Monovalent Salt Solution.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 3160
-
-
Garcia, A.E.1
Soumpasis, D.M.2
-
53
-
-
0347696834
-
Salt-Induced Conformational Changes in DNA: Analysis Using the Polymer RISM Theory
-
F. Hirata and R. M. Levy, J. Phys. Chem., 93, 479 (1989). Salt-Induced Conformational Changes in DNA: Analysis Using the Polymer RISM Theory.
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 479
-
-
Hirata, F.1
Levy, R.M.2
-
54
-
-
0000836584
-
Ionic Atmosphere of Rodlike Polyelectrolytes. a Hypernetted Chain Study
-
R. Bacquet and P. J. Rossky, J. Phys. Chem., 88, 2660 (1984). Ionic Atmosphere of Rodlike Polyelectrolytes. A Hypernetted Chain Study.
-
(1984)
J. Phys. Chem.
, vol.88
, pp. 2660
-
-
Bacquet, R.1
Rossky, P.J.2
-
55
-
-
0002705314
-
Hydration of Nucleic Acids
-
F. Franks, Ed., Cambridge University Press, Cambridge
-
E. Westhof and D. L. Beveridge, in Water Science Reviews, F. Franks, Ed., Cambridge University Press, Cambridge, 1990, pp. 24-123. Hydration of Nucleic Acids.
-
(1990)
Water Science Reviews
, pp. 24-123
-
-
Westhof, E.1
Beveridge, D.L.2
-
56
-
-
0000533571
-
Ionic Distributions and Competitive Association in DNA/Mixed Salt Solutions
-
R. J. Bacquet and P. J. Rossky, J. Phys. Chem., 92, 3604 (1988). Ionic Distributions and Competitive Association in DNA/Mixed Salt Solutions.
-
(1988)
J. Phys. Chem.
, vol.92
, pp. 3604
-
-
Bacquet, R.J.1
Rossky, P.J.2
-
57
-
-
0021753759
-
Potassium-39 NMR Study of Potassium Binding to Double Helical DNA
-
W. H. Braunlin and L. Nordenskiöld, Eur. J. Biochem., 142, 133 (1984). Potassium-39 NMR Study of Potassium Binding to Double Helical DNA.
-
(1984)
Eur. J. Biochem.
, vol.142
, pp. 133
-
-
Braunlin, W.H.1
Nordenskiöld, L.2
-
59
-
-
0027006826
-
Hexaamminecobalt(III) Binding Environments on Double-Helical DNA
-
W. H. Braunlin and Q. Xu, Biopolymers, 32, 1703 (1992). Hexaamminecobalt(III) Binding Environments on Double-Helical DNA.
-
(1992)
Biopolymers
, vol.32
, pp. 1703
-
-
Braunlin, W.H.1
Xu, Q.2
-
61
-
-
0022799313
-
Manganese-Deoxyribonucleic Acid Binding Modes
-
S. D. Kennedy and R. G. Bryant, Biophys. J., 50, 669 (1986). Manganese-Deoxyribonucleic Acid Binding Modes.
-
(1986)
Biophys. J.
, vol.50
, pp. 669
-
-
Kennedy, S.D.1
Bryant, R.G.2
-
62
-
-
0024328777
-
Laser Temperature-Jump, Spectroscopic, and Thermodynamic Study of Salt Effects on Duplex Formation by dGCATGC
-
A. P. Williams, C. E. Longfellow, S. M. Freier, R. Kierzek, and D. H. Turner, Biochemistry, 28, 4283 (1989). Laser Temperature-Jump, Spectroscopic, and Thermodynamic Study of Salt Effects on Duplex Formation by dGCATGC.
-
(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
-
63
-
-
0026909736
-
Differential Hydration of Homopurine Sequences Relative to Alternating Purine/Pyrimidine Sequences
-
D. Rentzeperis, D. W. Kupke, and L. A. Marky, Biopolymers, 32, 1065 (1992). Differential Hydration of Homopurine Sequences Relative to Alternating Purine/Pyrimidine Sequences.
-
(1992)
Biopolymers
, vol.32
, pp. 1065
-
-
Rentzeperis, D.1
Kupke, D.W.2
Marky, L.A.3
-
64
-
-
84986512474
-
CHARMM: A Program for Macromolecular Energy, Minimization, Dynamics Calculations
-
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem., 4, 187 (1983). CHARMM: A Program for Macromolecular Energy, Minimization, Dynamics Calculations.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
65
-
-
0024121512
-
Theoretical Considerations on the "Spine of Hydration" in the Minor Groove of d(CGCGAATTCGCG)·d(GCGCTTAAGCGC): Monte Carlo Computer Simulation
-
P. S. Subramanian, G. Ravishanker, and D. L. Beveridge, Proc. Natl. Acad. Sci. USA, 85, 1836 (1988). Theoretical Considerations on the "Spine of Hydration" in the Minor Groove of d(CGCGAATTCGCG)·d(GCGCTTAAGCGC): Monte Carlo Computer Simulation.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 1836
-
-
Subramanian, P.S.1
Ravishanker, G.2
Beveridge, D.L.3
-
66
-
-
85052507481
-
-
Clarendon Press, Oxford
-
M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987. J. M. Haile, Molecular Dynamics Simulation, Elementary Methods, Wiley, New York, 1992.
-
(1987)
Computer Simulation of Liquids
-
-
Allen, M.P.1
Tildesley, D.J.2
-
67
-
-
85052507481
-
-
Wiley, New York
-
M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987. J. M. Haile, Molecular Dynamics Simulation, Elementary Methods, Wiley, New York, 1992.
-
(1992)
Molecular Dynamics Simulation, Elementary Methods
-
-
Haile, J.M.1
-
68
-
-
84862582328
-
Computer Simulation of Biomolecular Systems Using Moleclular Dynamics and Free Energy Perturbation Methods
-
K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York
-
T. P. Lybrand, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 295-320. Computer Simulation of Biomolecular Systems Using Moleclular Dynamics and Free Energy Perturbation Methods. T. P. Straatsma, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 9, pp. 81-127. Free Energy by Molecular Simulation.
-
(1990)
Reviews in Computational Chemistry
, vol.1
, pp. 295-320
-
-
Lybrand, T.P.1
-
69
-
-
0030503687
-
Free Energy by Molecular Simulation
-
K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York
-
T. P. Lybrand, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 295-320. Computer Simulation of Biomolecular Systems Using Moleclular Dynamics and Free Energy Perturbation Methods. T. P. Straatsma, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 9, pp. 81-127. Free Energy by Molecular Simulation.
-
(1996)
Reviews in Computational Chemistry
, vol.9
, pp. 81-127
-
-
Straatsma, T.P.1
-
71
-
-
0004279414
-
-
University of California at San Francisco, CA
-
D. A. Pearlman D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, D. M. Ferguson, G. L. Seibel, U. C. Singh, P. Weiner, and P. Kollman, AMBER 4.1, 1995, University of California at San Francisco, CA.
-
(1995)
AMBER 4.1
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham T.E. III5
Ferguson, D.M.6
Seibel, G.L.7
Singh, U.C.8
Weiner, P.9
Kollman, P.10
-
72
-
-
33845790250
-
Molecular Dynamics of Liquid Water
-
A. Rahman and F. H. Stillinger, J. Chem. Phys., 55, 336 (1971). Molecular Dynamics of Liquid Water.
-
(1971)
J. Chem. Phys.
, vol.55
, pp. 336
-
-
Rahman, A.1
Stillinger, F.H.2
-
73
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys., 79, 926 (1983). Comparison of Simple Potential Functions for Simulating Liquid Water.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
75
-
-
0347920631
-
-
Wesleyan University, Middletown, CT
-
G. Ravishanker, S. Swaminathan, and D. L. Beveridge, WesDyn 2.0: Molecular Dynamics and Monte Carlo Stimulation for Proteins and DNA, Wesleyan University, Middletown, CT, 1994.
-
(1994)
WesDyn 2.0: Molecular Dynamics and Monte Carlo Stimulation for Proteins and DNA
-
-
Ravishanker, G.1
Swaminathan, S.2
Beveridge, D.L.3
-
76
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
-
W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz Jr., D. M. Ferguson D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am Chem. Soc., 117, 5179 (1995). A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules.
-
(1995)
J. Am Chem. Soc.
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz K.M., Jr.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
77
-
-
0025728614
-
OPLS Potential Functions for Nucleottde Bases. Relative Association Constants of Hydrogen-Bonded Base Pairs in Chloroform
-
J. Pranata, S. G. Wierschke, and W. L. Jorgensen, J. Am. Chem. Soc., 113, 2810 (1991). OPLS Potential Functions for Nucleottde Bases. Relative Association Constants of Hydrogen-Bonded Base Pairs in Chloroform.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 2810
-
-
Pranata, J.1
Wierschke, S.G.2
Jorgensen, W.L.3
-
78
-
-
33645941402
-
The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin
-
W. L. Jorgensen and J. Tirado-Rives, J. Am. Chem. Soc., 110, 1657 (1988). The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
79
-
-
0024795316
-
The Effects of Truncating Long-Range Forces on Protein Dynamics
-
R. J. Loncharich and B. R. Brooks, Proteins: Struct., Funct., Genet., 6, 32 (1989). The Effects of Truncating Long-Range Forces on Protein Dynamics.
-
(1989)
Proteins: Struct., Funct., Genet.
, vol.6
, pp. 32
-
-
Loncharich, R.J.1
Brooks, B.R.2
-
80
-
-
0026755515
-
Cutoff Size Does Strongly Influence Molecular Dynamics Results on Solvated Polypeptides
-
H. Schreiber and O. Steinhauser, Biochemistry, 31, 5856 (1992). Cutoff Size Does Strongly Influence Molecular Dynamics Results on Solvated Polypeptides.
-
(1992)
Biochemistry
, vol.31
, pp. 5856
-
-
Schreiber, H.1
Steinhauser, O.2
-
81
-
-
0000828880
-
A Simple Test for Evaluating the Truncation Effects in Simulation of Systems Involving Charged Groups
-
P. Auffinger and D. L. Beveridge, Chem. Phys. Lett., 234, 413 (1995). A Simple Test for Evaluating the Truncation Effects in Simulation of Systems Involving Charged Groups.
-
(1995)
Chem. Phys. Lett.
, vol.234
, pp. 413
-
-
Auffinger, P.1
Beveridge, D.L.2
-
82
-
-
0027484470
-
On Achieving Better than 1 Å Accuracy in a Simulation of a Large Protein: Streptomyces griseus Protease A
-
D. H. Kitson, F. Avbelj, J. Moult, D. T. Nguyen, J. E. Mertz, D. Hadzi, and A. T. Hagler, Proc. Natl. Acad. Sci. USA, 90, 8920 (1993). On Achieving Better than 1 Å Accuracy in a Simulation of a Large Protein: Streptomyces griseus Protease A.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 8920
-
-
Kitson, D.H.1
Avbelj, F.2
Moult, J.3
Nguyen, D.T.4
Mertz, J.E.5
Hadzi, D.6
Hagler, A.T.7
-
84
-
-
0028052906
-
A Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix: Evidence for Substates
-
K. J. McConnell, R. Nirmala, M. A. Young, G., Ravishanker, and D. L. Beveridge, J. Am. Chem. Soc., 116, 4461 (1994). A Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix: Evidence for Substates.
-
(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
-
85
-
-
84977266737
-
Die berechnung optischer und elektrostatischer Gitterpotentiale
-
P. Ewald, Ann. Phys. 64, 253 (1921). Die berechnung optischer und elektrostatischer Gitterpotentiale.
-
(1921)
Ann. Phys.
, vol.64
, pp. 253
-
-
Ewald, P.1
-
86
-
-
0001786236
-
Simulation of Electrostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants
-
S. W. de Leeuw, J. W. Perram, and E. R. Smith, Proc. R. Soc. London. A373, 27 (1980). Simulation of Electrostatic Systems in Periodic Boundary Conditions. I. Lattice Sums and Dielectric Constants.
-
(1980)
Proc. R. Soc. London. a
, vol.373
, pp. 27
-
-
De Leeuw, S.W.1
Perram, J.W.2
Smith, E.R.3
-
87
-
-
33846823909
-
Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems
-
T. A. Darden, D. M. York, and L. G. Pedersen, J. Chem. Phys., 98, 10089 (1993). Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089
-
-
Darden, T.A.1
York, D.M.2
Pedersen, L.G.3
-
88
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
U. Essmann, L. Perera, M. L. Berkowitz, T. A. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys., 103, 8577 (1995). A Smooth Particle Mesh Ewald Method.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.A.4
Lee, H.5
Pedersen, L.G.6
-
89
-
-
0029170114
-
Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
-
T. E. Cheatham III, J. L. Miller, T. Fox, T. A. Darden, and P. A. Kollman, J. Am. Chem. Soc., 117, 4193 (1995). Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4193
-
-
Cheatham T.E. III1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
90
-
-
0347920633
-
Nanosecond Molecular Dynamics Trajectories for a B-DNA Oligonucleotide Based on the AMBER 4.1 Force Field Including Water and Counterions
-
M. A. Young, G. Ravishanker, and D. L. Beveridge, Biophys. J., submitted (1997). Nanosecond Molecular Dynamics Trajectories for a B-DNA Oligonucleotide Based on the AMBER 4.1 Force Field Including Water and Counterions.
-
Biophys. J., Submitted
, pp. 1997
-
-
Young, M.A.1
Ravishanker, G.2
Beveridge, D.L.3
-
91
-
-
0000930430
-
Molecular Dynamics of B-DNA Including Water and Counterions: A 140 ps Trajectory for d(CGCGAATTCGCG) Based on the GROMOS Force Field
-
S. Swaminanthan, G. Ravishanker, and D. L. Beveridge, J. Am. Chem. Soc., 111, 5027 (1991). Molecular Dynamics of B-DNA Including Water and Counterions: A 140 ps Trajectory for d(CGCGAATTCGCG) Based on the GROMOS Force Field.
-
(1991)
J. Am. Chem. Soc.
, vol.111
, pp. 5027
-
-
Swaminanthan, S.1
Ravishanker, G.2
Beveridge, D.L.3
-
92
-
-
0024058085
-
The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids
-
R. Lavery and H. Sklenar, J. Biomol. Struct. Dyn., 6, 63 (1988). The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids.
-
(1988)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 63
-
-
Lavery, R.1
Sklenar, H.2
-
93
-
-
0024556774
-
Conformational and Helicoidal Analysis of 30 ps of Molecular Dynamics on the d(CGCGAATTCGCG) Double Helix: "Curves, Dials and Windows."
-
G. Ravishanker, S. Swaminathan, D. L. Beveridge, R. Lavery, and H. Sklenar, J. Biomol. Struct. Dyn., 6, 669 (1989). Conformational and Helicoidal Analysis of 30 ps of Molecular Dynamics on the d(CGCGAATTCGCG) Double Helix: "Curves, Dials and Windows."
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 669
-
-
Ravishanker, G.1
Swaminathan, S.2
Beveridge, D.L.3
Lavery, R.4
Sklenar, H.5
-
94
-
-
0026909824
-
A Molecular Dynamics Study of Conformational Changes and Hydration of Left-Handed d(CGCGCGCGCGCG), in a Nonsalt Solution
-
M. A. L. Eriksson and A. Laaksonen, Biopolymers, 32, 1035 (1992). A Molecular Dynamics Study of Conformational Changes and Hydration of Left-Handed d(CGCGCGCGCGCG), in a Nonsalt Solution.
-
(1992)
Biopolymers
, vol.32
, pp. 1035
-
-
Eriksson, M.A.L.1
Laaksonen, A.2
-
95
-
-
0025112951
-
Molecular Dynamics of an in Vacuo Model of Duplex d(CGCGAATTCGCG) in the B-Form Based on the AMBER 3.0 Force Field
-
J. Srinivasan, J. M. Withka, and D. L. Beveridge, Biophys. J., 58, 533 (1990). Molecular Dynamics of an In Vacuo Model of Duplex d(CGCGAATTCGCG) in the B-Form Based on the AMBER 3.0 Force Field.
-
(1990)
Biophys. J.
, vol.58
, pp. 533
-
-
Srinivasan, J.1
Withka, J.M.2
Beveridge, D.L.3
-
96
-
-
0027675937
-
Molecular Dynamics Simulations of poly(dA) -(dT): Comparisons between Implicit and Explicit Solvent Representations
-
V. Fritsch, G. Ravishanker, D. L. Beveridge, and E. Westhof, Biopolymers, 33, 1537 (1993). Molecular Dynamics Simulations of poly(dA) -(dT): Comparisons Between Implicit and Explicit Solvent Representations.
-
(1993)
Biopolymers
, vol.33
, pp. 1537
-
-
Fritsch, V.1
Ravishanker, G.2
Beveridge, D.L.3
Westhof, E.4
-
97
-
-
0027555852
-
Molecular Dynamic Simulations of B-DNA: An Analysis of the Role of Initial Molecular Configuration, Randomly Assigned Velocity Distribution, Long Integration Times, and Nonconstrained Termini
-
S. Falsafi and N. O. Reich, Biopolymers, 33, 459 (1993). Molecular Dynamic Simulations of B-DNA: An Analysis of the Role of Initial Molecular Configuration, Randomly Assigned Velocity Distribution, Long Integration Times, and Nonconstrained Termini.
-
(1993)
Biopolymers
, vol.33
, pp. 459
-
-
Falsafi, S.1
Reich, N.O.2
-
99
-
-
0000246675
-
Molecular Dynamics Studies of the Behavior of Water Molecules and Small Ions in Concentrated Solutions of Polymeric B-DNA
-
T. R. Forester and I. R. McDonald, Mol. Phys., 72, 643 (1991). Molecular Dynamics Studies of the Behavior of Water Molecules and Small Ions in Concentrated Solutions of Polymeric B-DNA.
-
(1991)
Mol. Phys.
, vol.72
, pp. 643
-
-
Forester, T.R.1
McDonald, I.R.2
-
100
-
-
0026019603
-
Molecular Dynamics Simulation of the Hydration Shell of a B-DNA Decamer Reveals Two Main Types of Minor-Groove Hydration Depending on Groove Width
-
V. P. Chuprina, U. Heinemann, A. A. Nurislamov, P. Zielenkiewicz, and R. E. Dickerson, Proc. Natl. Acad. Sci. USA, 88, 593 (1991). Molecular Dynamics Simulation of the Hydration Shell of a B-DNA Decamer Reveals Two Main Types of Minor-Groove Hydration Depending on Groove Width.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 593
-
-
Chuprina, V.P.1
Heinemann, U.2
Nurislamov, A.A.3
Zielenkiewicz, P.4
Dickerson, R.E.5
-
101
-
-
0024678912
-
A Theoretical Study of the Aqueous Hydration of Canonical B d(CGCGAATTCGCG): Monte Carlo Simulation and Comparison with Crystallographic Ordered Water Sites
-
P. S. Subramanian and D. L. Beveridge, J. Biomol. Struct. Dyn., 6, 1093 (1989). A Theoretical Study of the Aqueous Hydration of Canonical B d(CGCGAATTCGCG): Monte Carlo Simulation and Comparison with Crystallographic Ordered Water Sites.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 1093
-
-
Subramanian, P.S.1
Beveridge, D.L.2
-
103
-
-
0021383374
-
Monte Carlo Determination of the Distribution of Ions about a Cylindrical Polyelectrolyte
-
M. Le Bret and B. H. Zimm, Biopolymers, 23, 271 (1984). Monte Carlo Determination of the Distribution of Ions About a Cylindrical Polyelectrolyte.
-
(1984)
Biopolymers
, vol.23
, pp. 271
-
-
Le Bret, M.1
Zimm, B.H.2
-
104
-
-
33845378291
-
Ionic Distributions Near Polyelectrolytes: A Comparison of Theoretical Approaches
-
C. S. Murthy, R. J. Bacquet, and P. J. Rossky, J. Phys. Chem., 89, 701 (1985). Ionic Distributions Near Polyelectrolytes: A Comparison of Theoretical Approaches.
-
(1985)
J. Phys. Chem.
, vol.89
, pp. 701
-
-
Murthy, C.S.1
Bacquet, R.J.2
Rossky, P.J.3
-
105
-
-
0000001012
-
Monte Carlo Studies of Counterion-DNA Interactions. Comparison of the Radial Distribution of Counterions with Predictions of Other Polyelectrolyte Theories
-
P. Mills, C. F. Anderson, and M. T. Record Jr., J. Phys. Chem 89, 3984 (1985). Monte Carlo Studies of Counterion-DNA Interactions. Comparison of the Radial Distribution of Counterions with Predictions of Other Polyelectrolyte Theories.
-
(1985)
J. Phys. Chem
, vol.89
, pp. 3984
-
-
Mills, P.1
Anderson, C.F.2
Record M.T., Jr.3
-
106
-
-
0011264525
-
Monte Carlo Simulations of Counterion Accumulation Near Helical DNA
-
P. Mills, M. D. Paulsen, C. F. Anderson, and M. T. Record Jr., Chem. Phys. Lett. 129, 155 (1986). Monte Carlo Simulations of Counterion Accumulation Near Helical DNA.
-
(1986)
Chem. Phys. Lett.
, vol.129
, pp. 155
-
-
Mills, P.1
Paulsen, M.D.2
Anderson, C.F.3
Record M.T., Jr.4
-
107
-
-
0023777597
-
Counterion Exchange Reactions on DNA: Monte Carlo and Poisson-Boltzmann Analysis
-
M. D. Paulsen, C. F. Anderson, and M. T. Record Jr., Biopolymers, 27, 1249 (1988). Counterion Exchange Reactions on DNA: Monte Carlo and Poisson-Boltzmann Analysis.
-
(1988)
Biopolymers
, vol.27
, pp. 1249
-
-
Paulsen, M.D.1
Anderson, C.F.2
Record M.T., Jr.3
-
108
-
-
0024116002
-
Ions Around DNA: Monte Carlo Estimates of Distribution with Improved Electrostatic Potentials
-
J. Conrad, M. Troll, and B. H. Zimm, Biopolymers, 27, 1711 (1988). Ions Around DNA: Monte Carlo Estimates of Distribution with Improved Electrostatic Potentials.
-
(1988)
Biopolymers
, vol.27
, pp. 1711
-
-
Conrad, J.1
Troll, M.2
Zimm, B.H.3
-
109
-
-
0019843568
-
Structure of a B-DNA Dodecamer. 3. Geometry of Hydration
-
H. R. Drew and R. E. Dickerson, J. Mol. Biol., 151, 535 (1981). Structure of a B-DNA Dodecamer. 3. Geometry of Hydration.
-
(1981)
J. Mol. Biol.
, vol.151
, pp. 535
-
-
Drew, H.R.1
Dickerson, R.E.2
-
110
-
-
0021757436
-
A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins
-
S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner, J. Am. Chem. Soc., 106, 765 (1984). A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.8
-
111
-
-
84990406847
-
Dielectric Effects in Biopolymers: The Theory of Ionic Saturation Revisited
-
B. E. Hingerty, R. H. Ritchie, T. L. Ferrel, and J. E. Turner, Biopolymers, 24, 427 (1985). Dielectric Effects in Biopolymers: The Theory of Ionic Saturation Revisited.
-
(1985)
Biopolymers
, vol.24
, pp. 427
-
-
Hingerty, B.E.1
Ritchie, R.H.2
Ferrel, T.L.3
Turner, J.E.4
-
112
-
-
0000777707
-
Energetic Coupling between DNA Bending and Base Pair Opening
-
J. Ramstein and R. Lavery, Proc. Natl. Acad. Sci. USA, 85, 7231 (1988). Energetic Coupling Between DNA Bending and Base Pair Opening.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 7231
-
-
Ramstein, J.1
Lavery, R.2
-
113
-
-
0347920629
-
Simulations of the Counterion and Solvent Distribution Functions Around Two Simple Models of Polyelectrolyte
-
H. L. Gordon and S. Goldman, J. Phys. Chem., 96, 1921 (1992). Simulations of the Counterion and Solvent Distribution Functions Around Two Simple Models of Polyelectrolyte.
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 1921
-
-
Gordon, H.L.1
Goldman, S.2
-
114
-
-
0141531857
-
SPC Water Model
-
B. Pullman, Ed., Reidel, Dordrecht
-
H. J. C. Berendsen J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, in Intermolecular Forces Interaction Models for Water in Relation to Protein Hydration, B. Pullman, Ed., Reidel, Dordrecht, 1981, pp. 331-342. SPC Water Model.
-
(1981)
Intermolecular Forces Interaction Models for Water in Relation to Protein Hydration
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
116
-
-
0003438540
-
-
Cornell University Press, Ithaca, NY
-
L. Pauling, The Nature of the Chemical Bond, Third edition, Cornell University Press, Ithaca, NY, 1960.
-
(1960)
The Nature of the Chemical Bond, Third Edition
-
-
Pauling, L.1
-
117
-
-
36549096819
-
A Grand Canonical Monte Carlo Simulation Study of Polyelectrolyte Soutions
-
V. Vlachy and A. D. J. Haymet, J. Chem. Phys., 84, 5874 (1986). A Grand Canonical Monte Carlo Simulation Study of Polyelectrolyte Soutions.
-
(1986)
J. Chem. Phys.
, vol.84
, pp. 5874
-
-
Vlachy, V.1
Haymet, A.D.J.2
-
118
-
-
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
-
B. Jayaram and D. L. Beveridge, J. Phys. Chem., 95, 2506 (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.
-
(1991)
J. Phys. Chem.
, vol.95
, pp. 2506
-
-
Jayaram, B.1
Beveridge, D.L.2
-
119
-
-
0029110156
-
Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics
-
D. M. York, W. Yang, H. Lee, T. A. Darden, and L. G. Pedersen, J. Am. Chem. Soc 117, 5001 (1995). Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5001
-
-
York, D.M.1
Yang, W.2
Lee, H.3
Darden, T.A.4
Pedersen, L.G.5
-
120
-
-
0029139897
-
Nanosecond Dynamics and Structure of a Model DNA Triplex Helix in Saltwater Solution
-
S. Weerasinghe, P. E. Smith, V. Mohan, Y.-K. Cheng, and B. M. Petitt, J. Am. Chem. Soc., 117, 2147 (1995). Nanosecond Dynamics and Structure of a Model DNA Triplex Helix in Saltwater Solution.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 2147
-
-
Weerasinghe, S.1
Smith, P.E.2
Mohan, V.3
Cheng, Y.-K.4
Petitt, B.M.5
-
122
-
-
0025789088
-
The Dynemicin-DNA Intercalation Complex. a Model Based on DNA Affinity Cleavage and Molecular Dynamics Simulation
-
D. R. Langley, T. W. Doyle, and D. L. Beveridge, J. Am. Chem. Soc., 113, 4395 (1991). The Dynemicin-DNA Intercalation Complex. A Model Based on DNA Affinity Cleavage and Molecular Dynamics Simulation.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 4395
-
-
Langley, D.R.1
Doyle, T.W.2
Beveridge, D.L.3
-
123
-
-
0004720364
-
Molecular Dynamics Simulations of DNA and Protein-DNA Complexes Including Solvent
-
C. J. Cramer and D. G. Truhlar, Eds., ACS Symposiurn Series 568, American Chemical Society, Washington, D. C.
-
D. L. Beveridge K. J. McConnell, R. Nirmala, M. A. Young, S. Vijayakumar, and G. Ravishanker in Structure and Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems, C. J. Cramer and D. G. Truhlar, Eds., ACS Symposiurn Series 568, American Chemical Society, Washington, D. C., 1994, pp. 381-394. Molecular Dynamics Simulations of DNA and Protein-DNA Complexes Including Solvent.
-
(1994)
Structure and Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems
, pp. 381-394
-
-
Beveridge, D.L.1
McConnell, K.J.2
Nirmala, R.3
Young, M.A.4
Vijayakumar, S.5
Ravishanker, G.6
-
125
-
-
0007728014
-
Molecular Dynamics Simulations of d(CGCGA)*d(TCGCG) with and Without "Hydrated" Counterions
-
U. C. Singh, S. J. Weiner, and P. A. Kollman, Proc. Natl. Acad. Sci. USA. 82, 755 (1985). Molecular Dynamics Simulations of d(CGCGA)*d(TCGCG) With and Without "Hydrated" Counterions.
-
(1985)
Proc. Natl. Acad. Sci. USA.
, vol.82
, pp. 755
-
-
Singh, U.C.1
Weiner, S.J.2
Kollman, P.A.3
-
126
-
-
0001555216
-
A Molecular Dynamics Simulation of Double-Helical B-DNA Including Counterions and Water
-
G. L. Seibel, U. C. Singh, and P. A. Kollman, Proc. Natl. Acad. Sci. USA, 82, 6537 (1985). A Molecular Dynamics Simulation of Double-Helical B-DNA Including Counterions and Water.
-
(1985)
Proc. Natl. Acad. Sci. USA
, vol.82
, pp. 6537
-
-
Seibel, G.L.1
Singh, U.C.2
Kollman, P.A.3
-
127
-
-
0022838591
-
A Molecular Dynamics Computer Simulation of an Eight-Base-Pair DNA Fragment in Aqueous Solution: Comparison with Experimental Two-Dimensional NMR Data
-
W. F. van Gunsteren, H. J. C. Berendsen, R. G. Geurtsen, and H. R. J. Zwinderman, Ann. N. Y. Acad. Sci., 482, 287 (1986). A Molecular Dynamics Computer Simulation of an Eight-Base-Pair DNA Fragment in Aqueous Solution: Comparison with Experimental Two-Dimensional NMR Data.
-
(1986)
Ann. N. Y. Acad. Sci.
, vol.482
, pp. 287
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
Geurtsen, R.G.3
Zwinderman, H.R.J.4
-
129
-
-
0023449766
-
Hydration Structure and Dynamics of B- and Z-DNA in the Presence of Counterions Via Molecular Dynamics Simulations
-
K. N. Swamy and E. Clementi, Biopolymers, 26, 1901 (1987). Hydration Structure and Dynamics of B- and Z-DNA in the Presence of Counterions Via Molecular Dynamics Simulations.
-
(1987)
Biopolymers
, vol.26
, pp. 1901
-
-
Swamy, K.N.1
Clementi, E.2
-
130
-
-
0008025420
-
CI Study of the Water Dimer Potential Surface
-
O. Matsuoka, E. Clementi, and M. Yoshimine, J. Chem. Phys., 64, 1351 (1976). CI Study of the Water Dimer Potential Surface.
-
(1976)
J. Chem. Phys.
, vol.64
, pp. 1351
-
-
Matsuoka, O.1
Clementi, E.2
Yoshimine, M.3
-
131
-
-
0011210658
-
Molecular Dynamics Simulation of Double Helix Z-DNA in Solution
-
A. Laaksonen, L. G. Nilsson, B. Joensson, and O. Teleman, Chem. Phys., 129, 175 (1989). Molecular Dynamics Simulation of Double Helix Z-DNA in Solution.
-
(1989)
Chem. Phys.
, vol.129
, pp. 175
-
-
Laaksonen, A.1
Nilsson, L.G.2
Joensson, B.3
Teleman, O.4
-
132
-
-
0038737327
-
Structure of Aggregates of Water and Lithium, Sodium or Potassium Counterions with Nucleic Acid in Solution
-
E. Clementi and G. Corongiu, J. Biol. Phys., 11, 33 (1983). Structure of Aggregates of Water and Lithium, Sodium or Potassium Counterions with Nucleic Acid in Solution.
-
(1983)
J. Biol. Phys.
, vol.11
, pp. 33
-
-
Clementi, E.1
Corongiu, G.2
-
133
-
-
0025264049
-
Simulations of the B-DNA Molecular Dynamics of d(CGCGAATTCGCG) and d(CGCGCGCGCGCG): An Analysis of the Role of Initial Geometry and a Comparison of United and All-Atom Models
-
S. N. Rao and P. A. Kollman, Biopolymers, 29, 517 (1990). Simulations of the B-DNA Molecular Dynamics of d(CGCGAATTCGCG) and d(CGCGCGCGCGCG): An Analysis of the Role of Initial Geometry and a Comparison of United and All-Atom Models.
-
(1990)
Biopolymers
, vol.29
, pp. 517
-
-
Rao, S.N.1
Kollman, P.A.2
-
137
-
-
0026416497
-
A Molecular Dynamics Study of the Effect of G·T Mispairs of the Conformation of DNA in Solution
-
M. Shibata, T. J. Zielinski, and R. Rein, Biopolymers, 31, 211 (1991). A Molecular Dynamics Study of the Effect of G·T Mispairs of the Conformation of DNA in Solution.
-
(1991)
Biopolymers
, vol.31
, pp. 211
-
-
Shibata, M.1
Zielinski, T.J.2
Rein, R.3
-
138
-
-
0021376732
-
Energy Component Analysis for Dilute Aqueous Solutions of Li+, Na+, F-, and Cl-Ions
-
J. Chandrasekhar, D. C. Spellmeyer, and W. L. Jorgensen, J. Am Chem. Soc., 106, 903 (1984). Energy Component Analysis for Dilute Aqueous Solutions of Li+, Na+, F-, and Cl-Ions.
-
(1984)
J. Am Chem. Soc.
, vol.106
, pp. 903
-
-
Chandrasekhar, J.1
Spellmeyer, D.C.2
Jorgensen, W.L.3
-
139
-
-
37049068456
-
The Hydration Structure Around Chloride Ions in Aqueous Solution
-
D. H. Powell, A. C. Barnes, J. E. Enderby, G. W. Neilson, P. S. Salmon, Faraday Disc. Chem. Soc., 85, 137 (1988). The Hydration Structure Around Chloride Ions in Aqueous Solution.
-
(1988)
Faraday Disc. Chem. Soc.
, vol.85
, pp. 137
-
-
Powell, D.H.1
Barnes, A.C.2
Enderby, J.E.3
Neilson, G.W.4
Salmon, P.S.5
-
140
-
-
0347290413
-
Molecular Dynamics Simulations of DNA Oligomers under Various Electrostatic Parameters
-
V. Fritsch and E. Westhof, J. Chim. Phys., 88, 2543 (1991). Molecular Dynamics Simulations of DNA Oligomers Under Various Electrostatic Parameters.
-
(1991)
J. Chim. Phys.
, vol.88
, pp. 2543
-
-
Fritsch, V.1
Westhof, E.2
-
141
-
-
0000118937
-
Three Center Hydrogen Bonds in DNA: Molecular Dynamics of Poly(dA)*Poly(dT)
-
V. Fritsch and E. Westhof, J. Am. Chem. Soc., 113, 8271 (1991). Three Center Hydrogen Bonds in DNA: Molecular Dynamics of Poly(dA)*Poly(dT).
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 8271
-
-
Fritsch, V.1
Westhof, E.2
-
142
-
-
84986483814
-
Minimization and Molecular Dynamics Studies of Guanosine and Z-DNA Modified by N-2-Acetylaminofluorene
-
V. Fritsch and E. Westhof, J. Comput. Chem., 12, 147 (1991). Minimization and Molecular Dynamics Studies of Guanosine and Z-DNA Modified by N-2-Acetylaminofluorene.
-
(1991)
J. Comput. Chem.
, vol.12
, pp. 147
-
-
Fritsch, V.1
Westhof, E.2
-
143
-
-
0026900121
-
Conformational States of a TT Mismatch from Molecular Dynamics Simulation of Duplex d(CGCGATTCGCG)
-
R. M. Venable, G. Wildmalm, B. R. Brooks, W. Egan, and R. W. Pastor, Biopolymers, 32, 783 (1992). Conformational States of a TT Mismatch from Molecular Dynamics Simulation of Duplex d(CGCGATTCGCG).
-
(1992)
Biopolymers
, vol.32
, pp. 783
-
-
Venable, R.M.1
Wildmalm, G.2
Brooks, B.R.3
Egan, W.4
Pastor, R.W.5
-
144
-
-
0000935991
-
Molecular Dynamics Simulation of the Hydrated d (CGCGAATTCGCG) Dodecamer
-
K. Miaskiewicz, R. Osman, and H. Weinstein, J. Am. Chem. Soc., 115, 1526 (1992). Molecular Dynamics Simulation of the Hydrated d (CGCGAATTCGCG) Dodecamer.
-
(1992)
J. Am. Chem. Soc.
, vol.115
, pp. 1526
-
-
Miaskiewicz, K.1
Osman, R.2
Weinstein, H.3
-
145
-
-
0023663611
-
The Structure of poly(dA):poly(dT) in a Condensed State and in Solution
-
A. A. Lipanov and V. P. Chuprina, Nucleic Acid Res., 15, 5833 (1987). The Structure of poly(dA):poly(dT) in a Condensed State and in Solution.
-
(1987)
Nucleic Acid Res.
, vol.15
, pp. 5833
-
-
Lipanov, A.A.1
Chuprina, V.P.2
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