-
2
-
-
0033150892
-
DNA structure: Cations in charge
-
McFail-Isom, L., Sines, C.C., Williams, L.D. (1999) DNA structure: cations in charge Curr. Opin. Struct. Biol., 9, 298-304.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 298-304
-
-
McFail-Isom, L.1
Sines, C.C.2
Williams, L.D.3
-
3
-
-
0023708040
-
Water: An integral part of nucleic acid structure
-
Westhof, E. (1988) Water: an integral part of nucleic acid structure. Annu. Rev. Biophys. Biophys. Chem., 17, 125-144.
-
(1988)
Annu. Rev. Biophys. Biophys. Chem.
, vol.17
, pp. 125-144
-
-
Westhof, E.1
-
4
-
-
66649116808
-
Nonspecific DNA-protein interaction: Why proteins can diffuse along DNA
-
Dahirel, V., Paillusson, F., Jardat, M., Barbi, M., Victor, J.M. (2009) Nonspecific DNA-protein interaction: why proteins can diffuse along DNA. Phys. Rev. Lett., 102, 228101.
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 228101
-
-
Dahirel, V.1
Paillusson, F.2
Jardat, M.3
Barbi, M.4
Victor, J.M.5
-
5
-
-
34247272005
-
The DNA structure responds differently to physiological concentrations of K(+) or Na(+)
-
Heddi, B., Foloppe, N., Hantz, E., Hartmann, B. (2007) The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J. Mol. Biol., 368, 1403-1411.
-
(2007)
J. Mol. Biol.
, vol.368
, pp. 1403-1411
-
-
Heddi, B.1
Foloppe, N.2
Hantz, E.3
Hartmann, B.4
-
6
-
-
0017895903
-
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
-
Manning, G.S. (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys., 11, 179-246.
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 179-246
-
-
Manning, G.S.1
-
7
-
-
0025308916
-
Ion distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications
-
Anderson, C.F., Record, M.T. Jr (1990) Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. Annu. Rev. Biophys. Biophys. Chem., 19, 423-463.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 423-463
-
-
Anderson, C.F.1
Record, M.T.2
-
8
-
-
56249129385
-
Sequence-specific DNA-metal ion interactions
-
Royal Society of Chemistry London
-
Hud, N.V., Engelhart, A.E. (2009) Sequence-specific DNA-metal ion interactions. In: Nucleic Acid-Metal Ion Interactions. Royal Society of Chemistry, London, Vol. 14, pp. 75-117.
-
(2009)
Nucleic Acid-Metal Ion Interactions
, vol.14
, pp. 75-117
-
-
Hud, N.V.1
Engelhart, A.E.2
-
9
-
-
0035964383
-
Locating monovalent cations in the grooves of B-DNA
-
Howerton, S.B., Sines, C.C., VanDerveer, D., Williams, L.D. (2001) Locating monovalent cations in the grooves of B-DNA. Biochemistry, 40, 10023-10031.
-
(2001)
Biochemistry
, vol.40
, pp. 10023-10031
-
-
Howerton, S.B.1
Sines, C.C.2
VanDerveer, D.3
Williams, L.D.4
-
10
-
-
0035283086
-
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments
-
Tereshko, V., Wilds, C.J., Minasov, G., Prakash, T.P., Maier, M.A., Howard, A., Wawrzak, Z., Manoharan, M., Egli, M. (2001) Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. Nucleic Acids Res., 29, 1208-1215.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 1208-1215
-
-
Tereshko, V.1
Wilds, C.J.2
Minasov, G.3
Prakash, T.P.4
Maier, M.A.5
Howard, A.6
Wawrzak, Z.7
Manoharan, M.8
Egli, M.9
-
11
-
-
0034327565
-
Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
-
Hamelberg, D., McFail-Isom, L., Williams, L.D., Wilson, W.D. (2000) Flexible structure of DNA: ion dependence of minor-groove structure and dynamics. J. Am. Chem. Soc., 122, 10513-10520.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 10513-10520
-
-
Hamelberg, D.1
McFail-Isom, L.2
Williams, L.D.3
Wilson, W.D.4
-
12
-
-
0034005285
-
Monovalent cations sequester within the A-tract minor groove of [d(CGCGAATTCGCG)]2 †§
-
Woods, K.K., McFail-Isom, L., Sines, C.C., Howerton, S.B., Stephens, R.K., Williams, L.D. (2000) Monovalent cations sequester within the A-tract minor groove of [d(CGCGAATTCGCG)]2 †, §. J. Am. Chem. Soc., 122, 1546-1547.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 1546-1547
-
-
Woods, K.K.1
McFail-Isom, L.2
Sines, C.C.3
Howerton, S.B.4
Stephens, R.K.5
Williams, L.D.6
-
13
-
-
0033585580
-
The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution
-
Tereshko, V., Minasov, G., Egli, M. (1999) The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J. Am. Chem. Soc., 121, 470-471.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 470-471
-
-
Tereshko, V.1
Minasov, G.2
Egli, M.3
-
14
-
-
0033600794
-
Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG
-
Chiu, T.K., Kaczor-Grzeskowiak, M., Dickerson, R.E. (1999) Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG. J. Mol. Biol., 292, 589-608.
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 589-608
-
-
Chiu, T.K.1
Kaczor-Grzeskowiak, M.2
Dickerson, R.E.3
-
15
-
-
0033605083
-
Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
-
Hud, N.V., Sklenr, V., Feigon, J. (1999) Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J. Mol. Biol., 286, 651-660.
-
(1999)
J. Mol. Biol.
, vol.286
, pp. 651-660
-
-
Hud, N.V.1
Sklenr, V.2
Feigon, J.3
-
16
-
-
79955846859
-
SAXS studies of ion-nucleic acid interactions
-
Pollack, L. (2011) SAXS studies of ion-nucleic acid interactions. Annu. Rev. Biophys., 40, 225-242.
-
(2011)
Annu. Rev. Biophys.
, vol.40
, pp. 225-242
-
-
Pollack, L.1
-
17
-
-
84902148550
-
Understanding nucleic acid-ion interactions
-
Lipfert, J., Doniach, S., Das, R., Herschlag, D. (2014) Understanding nucleic acid-ion interactions. Annu. Rev. Biochem., 83, 813-841.
-
(2014)
Annu. Rev. Biochem.
, vol.83
, pp. 813-841
-
-
Lipfert, J.1
Doniach, S.2
Das, R.3
Herschlag, D.4
-
18
-
-
0034681195
-
Sequence-specific binding of counterions to B-DNA
-
Denisov, V.P., Halle, B. (2000) Sequence-specific binding of counterions to B-DNA. Proc. Natl. Acad. Sci. U.S.A., 97, 629-633.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 629-633
-
-
Denisov, V.P.1
Halle, B.2
-
19
-
-
2542583798
-
Competitive Na(+) and Rb(+) binding in the minor groove of DNA
-
Cesare Marincola, F., Denisov, V.P., Halle, B. (2004) Competitive Na(+) and Rb(+) binding in the minor groove of DNA. J. Am. Chem. Soc., 126, 6739-6750.
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 6739-6750
-
-
Cesare Marincola, F.1
Denisov, V.P.2
Halle, B.3
-
20
-
-
0031047279
-
Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
-
Young, M.A., Jayaram, B., Beveridge, D.L. (1997) Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets. J. Am. Chem. Soc., 119, 59-69.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 59-69
-
-
Young, M.A.1
Jayaram, B.2
Beveridge, D.L.3
-
21
-
-
34347404466
-
Nucleic acid solvation: From outside to insight
-
Auffinger, P., Hashem, Y. (2007) Nucleic acid solvation: from outside to insight. Curr. Opin. Struct. Biol., 17, 325-333.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 325-333
-
-
Auffinger, P.1
Hashem, Y.2
-
22
-
-
84865511740
-
Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is worth its salt
-
Mocci, F., Laaksonen, A. (2012) Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is "worth its salt". Soft Matter, 8, 9268-9284.
-
(2012)
Soft Matter
, vol.8
, pp. 9268-9284
-
-
Mocci, F.1
Laaksonen, A.2
-
23
-
-
84902971502
-
Polarizable empirical force field for hexopyranose monosaccharides based on the classical drude oscillator
-
Patel, D.S., He, X., MacKerell, A.D. (2014) Polarizable empirical force field for hexopyranose monosaccharides based on the classical drude oscillator. J. Phys. Chem. B., 119, 637-652.
-
(2014)
J. Phys. Chem. B.
, vol.119
, pp. 637-652
-
-
Patel, D.S.1
He, X.2
MacKerell, A.D.3
-
24
-
-
4043179941
-
DNA and its counterions: A molecular dynamics study
-
Vrnai, P., Zakrzewska, K. (2004) DNA and its counterions: a molecular dynamics study. Nucleic Acids Re., 32, 4269-4280.
-
(2004)
Nucleic Acids Re.
, vol.32
, pp. 4269-4280
-
-
Vrnai, P.1
Zakrzewska, K.2
-
25
-
-
4143138536
-
Exploring the counterion atmosphere around DNA: What can be learned from molecular dynamics simulations
-
Rueda, M., Cubero, E., Laughton, C.A., Orozco, M. (2004) Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations Biophys. J., 87, 800-811.
-
(2004)
Biophys J
, vol.87
, pp. 800-811
-
-
Rueda, M.1
Cubero, E.2
Laughton, C.A.3
Orozco, M.4
-
26
-
-
0035793219
-
Water and ion binding around r(UpA) 12 and d(TpA)12 oligomers-comparison with RNA and DNA (CpG)12 duplexes
-
Auffinger, P., Westhof, E. (2001) Water and ion binding around r(UpA)12 and d(TpA)12 oligomers-comparison with RNA and DNA (CpG)12 duplexes. J. Mol. Biol., 305, 1057-1072.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 1057-1072
-
-
Auffinger, P.1
Westhof, E.2
-
27
-
-
0034725528
-
Water and ion binding around RNA and DNA (C, G) oligomers
-
Auffinger, P., Westhof, E. (2000) Water and ion binding around RNA and DNA (C, G) oligomers. J. Mol. Biol., 300, 1113-1131.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 1113-1131
-
-
Auffinger, P.1
Westhof, E.2
-
28
-
-
84864375687
-
Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations
-
Dixit, S.B., Mezei, M., Beveridge, D.L. (2012) Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations. J. Biosci., 37, 399-421.
-
(2012)
J. Biosci.
, vol.37
, pp. 399-421
-
-
Dixit, S.B.1
Mezei, M.2
Beveridge, D.L.3
-
29
-
-
0032851951
-
Sodium and chlorine ions as part of the DNA solvation shell
-
Feig, M., Pettitt, B.M. (1999) Sodium and chlorine ions as part of the DNA solvation shell. Biophys. J., 77, 1769-1781.
-
(1999)
Biophys. J.
, vol.77
, pp. 1769-1781
-
-
Feig, M.1
Pettitt, B.M.2
-
31
-
-
6944220065
-
Ion motions in molecular dynamics simulations on DNA
-
Ponomarev, S.Y., Thayer, K.M., Beveridge, D.L. (2004) Ion motions in molecular dynamics simulations on DNA. Proc. Natl. Acad. Sci. U.S.A., 101, 14771-14775.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 14771-14775
-
-
Ponomarev, S.Y.1
Thayer, K.M.2
Beveridge, D.L.3
-
32
-
-
36749098380
-
Dynamics of B-DNA on the microsecond time scale
-
Prez, A., Luque, F.J., Orozco, M. (2007) Dynamics of B-DNA on the microsecond time scale. J. Am. Chem. Soc., 129, 14739-14745.
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 14739-14745
-
-
Prez, A.1
Luque, F.J.2
Orozco, M.3
-
33
-
-
84922390477
-
Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA
-
Dans, P.D., Faustino, I., Battistini, F., Zakrzewska, K., Lavery, R., Orozco, M. (2014) Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA. Nucleic Acids Res., 42, 11304-11320.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 11304-11320
-
-
Dans, P.D.1
Faustino, I.2
Battistini, F.3
Zakrzewska, K.4
Lavery, R.5
Orozco, M.6
-
34
-
-
84870578921
-
Exploring polymorphisms in B-DNA helical conformations
-
Dans, P.D., Perez, A., Faustino, I., Lavery, R., Orozco, M. (2012) Exploring polymorphisms in B-DNA helical conformations. Nucleic Acids Res., 40, 10668-10678.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 10668-10678
-
-
Dans, P.D.1
Perez, A.2
Faustino, I.3
Lavery, R.4
Orozco, M.5
-
35
-
-
40849094011
-
Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method
-
Min, D., Li, H., Li, G., Berg, B.A., Fenley, M.O., Yang, W. (2008) Efficient sampling of ion motions in molecular dynamics simulations on DNA: variant Hamiltonian replica exchange method. Chem. Phys. Lett., 454, 391-395.
-
(2008)
Chem. Phys. Lett.
, vol.454
, pp. 391-395
-
-
Min, D.1
Li, H.2
Li, G.3
Berg, B.A.4
Fenley, M.O.5
Yang, W.6
-
36
-
-
84857256519
-
The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations
-
Kirmizialtin, S., Silalahi, A.R., Elber, R., Fenley, M.O. (2012) The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations. Biophys. J., 102, 829-838.
-
(2012)
Biophys. J.
, vol.102
, pp. 829-838
-
-
Kirmizialtin, S.1
Silalahi, A.R.2
Elber, R.3
Fenley, M.O.4
-
37
-
-
84894410481
-
Ion counting from explicit-solvent simulations and 3D-RISM
-
Giambas, G.M., Luchko, T., Herschlag, D., York, D.M., Case, D.A. (2014) Ion counting from explicit-solvent simulations and 3D-RISM. Biophys. J., 106, 883-894.
-
(2014)
Biophys. J.
, vol.106
, pp. 883-894
-
-
Giambas, G.M.1
Luchko, T.2
Herschlag, D.3
York, D.M.4
Case, D.A.5
-
38
-
-
78751654619
-
Ion and solvent density distributions around canonical B-DNA from integral equations
-
Howard, J.J., Lynch, G.C., Pettitt, B.M. (2011) Ion and solvent density distributions around canonical B-DNA from integral equations. J. Phys. Chem. B, 115, 547-556.
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 547-556
-
-
Howard, J.J.1
Lynch, G.C.2
Pettitt, B.M.3
-
39
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
-
Prez, A., Marchn, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A., Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Prez, A.1
Marchn, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
40
-
-
0029636784
-
Mechanism and thermodynamics of ion selectivity in aqueous-solutions of 18-crown-6 ether-a molecular dynamics study
-
Dang, L.X. (1995) Mechanism and thermodynamics of ion selectivity in aqueous-solutions of 18-crown-6 ether-a molecular dynamics study. J. Am. Chem. Soc., 117, 6954-6960.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 6954-6960
-
-
Dang, L.X.1
-
41
-
-
84860477162
-
Frontiers in molecular dynamics simulations of DNA
-
Prez, A., Luque, F.J., Orozco, M. (2012) Frontiers in molecular dynamics simulations of DNA. Acc. Chem. Res., 45, 196-205.
-
(2012)
Acc. Chem. Res.
, vol.45
, pp. 196-205
-
-
Prez, A.1
Luque, F.J.2
Orozco, M.3
-
42
-
-
84923151437
-
ABC: A systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
-
Pasi, M., Maddocks, J.H., Beveridge, D., Bishop, T.C., Case, D.A., Cheatham, T., Dans, P.D., Jayaram, B., Lankas, F. et al. (2014)-ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Res., 42, 12272-12283.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 12272-12283
-
-
Pasi, M.1
Maddocks, J.H.2
Beveridge, D.3
Bishop, T.C.4
Case, D.A.5
Cheatham, T.6
Dans, P.D.7
Jayaram, B.8
Lankas, F.9
-
43
-
-
84903957372
-
Analyzing ion distributions around DNA
-
Lavery, R., Maddocks, J.H., Pasi, M., Zakrzewska, K. (2014) Analyzing ion distributions around DNA. Nucleic Acids Res., 42, 8138-8149.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 8138-8149
-
-
Lavery, R.1
Maddocks, J.H.2
Pasi, M.3
Zakrzewska, K.4
-
44
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., DeBolt, S., Ferguson, D., Seibel, G., Kollman, P. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun., 91, 1-41.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
DeBolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
45
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B., Woods, R.J. (2005) The Amber biomolecular simulation programs. J. Comput. Chem., 26, 1668-1688.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
46
-
-
0032922174
-
A modified version of the Cornell et al. Force field with improved sugar pucker phases and helical repeat
-
Cheatham, T.E. 3rd, Cieplak, P., Kollman, P.A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn., 16, 845-862.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 845-862
-
-
Cheatham, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
47
-
-
1242346370
-
The missing term in effective pair potentials
-
Berendsen, H.J.C., Grigera, J.R., Straatsma, T.P. (1987) The missing term in effective pair potentials. J. Phys. Chem., 91, 6269-6271.
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.J.C.1
Grigera, J.R.2
Straatsma, T.P.3
-
48
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., Pedersen, L.G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys., 103, 8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
49
-
-
70450248170
-
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
-
Lavery, R., Zakrzewska, K., Beveridge, D., Bishop, T.C., Case, D.A., Cheatham, T., Dixit, S., Jayaram, B., Lankas, F., Laughton, C. et al. (2010) A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res., 38, 299-313.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 299-313
-
-
Lavery, R.1
Zakrzewska, K.2
Beveridge, D.3
Bishop, T.C.4
Case, D.A.5
Cheatham, T.6
Dixit, S.7
Jayaram, B.8
Lankas, F.9
Laughton, C.10
-
50
-
-
28444490422
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
-
Dixit, S.B., Beveridge, D.L., Case, D.A., Cheatham, T.E. 3rd, Giudice, E., Lankas, F., Lavery, R., Maddocks, J.H., Osman, R. (2005) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys. J., 89, 3721-3740.
-
(2005)
Biophys. J.
, vol.89
, pp. 3721-3740
-
-
Dixit, S.B.1
Beveridge, D.L.2
Case, D.A.3
Cheatham, T.E.4
Giudice, E.5
Lankas, F.6
Lavery, R.7
Maddocks, J.H.8
Osman, R.9
-
51
-
-
10044257912
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps
-
Beveridge, D.L., Barreiro, G., Byun, K.S., Case, D.A., Cheatham, T.E. 3rd, Dixit, S.B., Giudice, E., Lankas, F., Lavery, R. (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys. J., 87, 3799-3813.
-
(2004)
Biophys. J.
, vol.87
, pp. 3799-3813
-
-
Beveridge, D.L.1
Barreiro, G.2
Byun, K.S.3
Case, D.A.4
Cheatham, T.E.5
Dixit, S.B.6
Giudice, E.7
Lankas, F.8
Lavery, R.9
-
52
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., Haak, J.R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
53
-
-
33646940952
-
Numerical-integration of cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes
-
Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C. (1977) Numerical-integration of cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes. J. Comput. Phys., 23, 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
54
-
-
0001430231
-
The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
-
Harvey, S.C., Tan, R.K.Z., Cheatham, T.E. III (1998) The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J. Comput. Chem., 19, 726-740.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 726-740
-
-
Harvey, S.C.1
Tan, R.K.Z.2
Cheatham, T.E.3
-
55
-
-
79959930132
-
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures
-
Blanchet, C., Pasi, M., Zakrzewska, K., Lavery, R. (2011) CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures. Nucleic Acids Res., 39, W68-W73.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W68-W73
-
-
Blanchet, C.1
Pasi, M.2
Zakrzewska, K.3
Lavery, R.4
-
56
-
-
70450261721
-
Conformational analysis of nucleic acids revisited: Curves+
-
Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D., Zakrzewska, K. (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res., 37, 5917-5929.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5917-5929
-
-
Lavery, R.1
Moakher, M.2
Maddocks, J.H.3
Petkeviciute, D.4
Zakrzewska, K.5
-
57
-
-
11644276439
-
Limiting laws and counterion condensation in polyelectrolyte solutions I. Colligative properties
-
Manning, G.S. (1969) Limiting laws and counterion condensation in polyelectrolyte solutions I. Colligative properties. J. Chem. Phys., 51, 924-933.
-
(1969)
J. Chem. Phys.
, vol.51
, pp. 924-933
-
-
Manning, G.S.1
-
58
-
-
34247500374
-
Python for scientific computing
-
Oliphant, T.E.
-
Oliphant, T.E. (2007) Python for scientific computing. Comput. Sci. Eng., 9, 10-20.
-
(2007)
Comput. Sci. Eng.
, vol.9
, pp. 10-20
-
-
-
59
-
-
34247493236
-
Matplotlib: A 2D graphics environment
-
Hunter, J.D. (2007) Matplotlib: a 2D graphics environment. Comput. Sci. Eng., 9, 90-95.
-
(2007)
Comput. Sci. Eng.
, vol.9
, pp. 90-95
-
-
Hunter, J.D.1
-
60
-
-
33845345287
-
Visualizing density maps with UCSF Chimera
-
Goddard, T.D., Huang, C.C., Ferrin, T.E. (2007) Visualizing density maps with UCSF Chimera. J. Struct. Biol., 157, 281-287.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 281-287
-
-
Goddard, T.D.1
Huang, C.C.2
Ferrin, T.E.3
-
61
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
62
-
-
84984062480
-
Molecular electrostatic potential on the surface envelopes of macromolecules: B-DNA
-
Lavery, R., Pullman, B. (1981) Molecular electrostatic potential on the surface envelopes of macromolecules: B-DNA. Int. J. Quant. Chem., 20, 259-272.
-
(1981)
Int. J. Quant. Chem.
, vol.20
, pp. 259-272
-
-
Lavery, R.1
Pullman, B.2
-
63
-
-
0024580271
-
The electrostatic potential of B-DNA
-
Jayaram, B., Sharp, K.A., Honig, B. (1989) The electrostatic potential of B-DNA. Biopolymers, 28, 975-993.
-
(1989)
Biopolymers
, vol.28
, pp. 975-993
-
-
Jayaram, B.1
Sharp, K.A.2
Honig, B.3
-
64
-
-
84860376513
-
B-DNA structure is intrinsically polymorphic: Even at the level of base pair positions
-
Maehigashi, T., Hsiao, C., Woods, K.K., Moulaei, T., Hud, N.V., Williams, L.D. (2012) B-DNA structure is intrinsically polymorphic: even at the level of base pair positions. Nucleic Acids Res., 40, 3714-3722.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 3714-3722
-
-
Maehigashi, T.1
Hsiao, C.2
Woods, K.K.3
Moulaei, T.4
Hud, N.V.5
Williams, L.D.6
-
65
-
-
0021959842
-
The molecular origin of DNA-drug specificity in netropsin and distamycin
-
Kopka, M.L., Yoon, C., Goodsell, D., Pjura, P., Dickerson, R.E. (1985) The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc. Natl. Acad. Sci. U.S.A., 82, 1376-1380.
-
(1985)
Proc. Natl. Acad. Sci. U.S.A.
, vol.82
, pp. 1376-1380
-
-
Kopka, M.L.1
Yoon, C.2
Goodsell, D.3
Pjura, P.4
Dickerson, R.E.5
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