54
M. P. Evstigneev and A. V. Shestopalova
64. Dukhopelnikov EV, Bereznyak EG, Khrebtova AS, Lantushenko AO, Zinchenko AV (2012)
Determination of ligand to DNA binding parameters from two-dimensional DSC curves. J
Therm Anal Calorim. doi:10.1007/s10973–012-2561–6
65. Orozco M, Luque FJ (2000) Theoretical methods for the description of the solvent effect in
biomolecular systems. Chem Rev 100(11):4187–4225
66. Lazaridis T (2002) Binding affinity and specificity from computational studies. Cur Organ
Chem 6(14):1319–1332
67. Schlick T (2010) Molecular modelling and simulation: an interdisciplinary guide, 2nd edn.
Springer, New York
68. Cheatham TE III (2004) Simulation and modeling of nucleic acid structure, dynamics and
interactions. Curr Opin Struct Biol 14(3):360–367
69. Dolenc J, Oostenbrink Ch, Koller J, van Gunsteren WF (2005) Molecular dynamics simulation and free energy calculations of netropsin and distamycin binding to AAAAA DNA
binding site. Nucleic Acids Res 33(2):725–733
70. Ruiz R, García B, Ruisi G, Silvestri A, Barone G (2009) Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2. J Mol Struct: THEOCHEM 915(1):86–92
71. Sasikala WD, Mukherjee A (2012) Molecular mechanism of direct proflavine–DNA Intercalation: evidence for drug-induced minimum base-stacking penalty pathway. J Phys Chem
B 116(40):12208–12212
72. Schneider G, Bohm H-J (2002) Virtual screening and fast automated docking methods.
Drug Discov Today 7(1):64–70
73. Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: an overview of
search algorithms and a guide to scoring functions. Proteins 47 (4):409–415
74. Smith GR, Sternberg MJE (2002) Prediction of protein–protein interactions by docking
methods. Curr Opin Struct Biol 12(1):28–35
75. Lauria A, Diana P, Barraja P, Montalbano A, Dattolo G, Cirrincione G (2004) Docking of
indolo- and pyrrolo-pyrimidines to DNA. New DNA-interactive polycycles from aminoindoles/pyrroles and BMMA. ARKIVOC 5(2):263–271
76. Miroshnychenko KV, Shestopalova AV (2010) The effect of drug-DNA interactions on the
intercalation site formation. Int J Quant Chem 110(1):161–176
77. Danilov VI, Tolokh IS (1990) Hydration of uracil and thymine methylderivatives: a Monte
Carlo simulation. J Biomol Struct Dyn 7(5):1167–1183
78. Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL (1997) The study of
the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by the Monte Carlo method. J Biomol Struct Dyn 15(1):69–80
79. Teplukhin AV, Malenkov GG, Poltev VI (1998) Monte Carlo simulation of DNA fragment
hydration in the presence of alkaline cations using novel atom-atom potential functions. J
Biomol Struct Dyn 16(2):289–300
80. Alderfer JL, Danilov VI, Poltev VI, Slyusarchuk ON (1999) A study of the hydration of deoxydinucleoside monophosphates containing thymine, uracil and its 5-halogen derivatives:
Monte Carlo simulation. J Biomol Struct Dyn 16(5):1107–1117
81. Resat H, Mezei M (1996) Grand canonical ensemble Monte Carlo simulation of the dCpG/
proflavine crystal hydrate. Biophysical J 71(3):1179–1190
82. Alcaro S, Coleman RS (2000) A molecular model for DNA cross-linking by the antitumor
agent azinomycin B. J Med Chem 43(15):2783–2788
83. Shestopalova AV (2002) Hydration of nucleic acids components in dependence of nucleotide composition and relative humidity: a Monte Carlo simulation. Europ Phys J D
20(1):331–337
84. Shestopalova AV (2007) The binding of actinocin derivative with DNA fragments (Monte
Carlo simulation). Biopolym Cell 23(1):35–44
85. Auffinger P, Westhof E (1997) Molecular dynamics: simulations of nucleic acids. Rev
Comp Chem 11(2):317–328
M. P. Evstigneev and A. V. Shestopalova
64. Dukhopelnikov EV, Bereznyak EG, Khrebtova AS, Lantushenko AO, Zinchenko AV (2012)
Determination of ligand to DNA binding parameters from two-dimensional DSC curves. J
Therm Anal Calorim. doi:10.1007/s10973–012-2561–6
65. Orozco M, Luque FJ (2000) Theoretical methods for the description of the solvent effect in
biomolecular systems. Chem Rev 100(11):4187–4225
66. Lazaridis T (2002) Binding affinity and specificity from computational studies. Cur Organ
Chem 6(14):1319–1332
67. Schlick T (2010) Molecular modelling and simulation: an interdisciplinary guide, 2nd edn.
Springer, New York
68. Cheatham TE III (2004) Simulation and modeling of nucleic acid structure, dynamics and
interactions. Curr Opin Struct Biol 14(3):360–367
69. Dolenc J, Oostenbrink Ch, Koller J, van Gunsteren WF (2005) Molecular dynamics simulation and free energy calculations of netropsin and distamycin binding to AAAAA DNA
binding site. Nucleic Acids Res 33(2):725–733
70. Ruiz R, García B, Ruisi G, Silvestri A, Barone G (2009) Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2. J Mol Struct: THEOCHEM 915(1):86–92
71. Sasikala WD, Mukherjee A (2012) Molecular mechanism of direct proflavine–DNA Intercalation: evidence for drug-induced minimum base-stacking penalty pathway. J Phys Chem
B 116(40):12208–12212
72. Schneider G, Bohm H-J (2002) Virtual screening and fast automated docking methods.
Drug Discov Today 7(1):64–70
73. Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: an overview of
search algorithms and a guide to scoring functions. Proteins 47 (4):409–415
74. Smith GR, Sternberg MJE (2002) Prediction of protein–protein interactions by docking
methods. Curr Opin Struct Biol 12(1):28–35
75. Lauria A, Diana P, Barraja P, Montalbano A, Dattolo G, Cirrincione G (2004) Docking of
indolo- and pyrrolo-pyrimidines to DNA. New DNA-interactive polycycles from aminoindoles/pyrroles and BMMA. ARKIVOC 5(2):263–271
76. Miroshnychenko KV, Shestopalova AV (2010) The effect of drug-DNA interactions on the
intercalation site formation. Int J Quant Chem 110(1):161–176
77. Danilov VI, Tolokh IS (1990) Hydration of uracil and thymine methylderivatives: a Monte
Carlo simulation. J Biomol Struct Dyn 7(5):1167–1183
78. Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL (1997) The study of
the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by the Monte Carlo method. J Biomol Struct Dyn 15(1):69–80
79. Teplukhin AV, Malenkov GG, Poltev VI (1998) Monte Carlo simulation of DNA fragment
hydration in the presence of alkaline cations using novel atom-atom potential functions. J
Biomol Struct Dyn 16(2):289–300
80. Alderfer JL, Danilov VI, Poltev VI, Slyusarchuk ON (1999) A study of the hydration of deoxydinucleoside monophosphates containing thymine, uracil and its 5-halogen derivatives:
Monte Carlo simulation. J Biomol Struct Dyn 16(5):1107–1117
81. Resat H, Mezei M (1996) Grand canonical ensemble Monte Carlo simulation of the dCpG/
proflavine crystal hydrate. Biophysical J 71(3):1179–1190
82. Alcaro S, Coleman RS (2000) A molecular model for DNA cross-linking by the antitumor
agent azinomycin B. J Med Chem 43(15):2783–2788
83. Shestopalova AV (2002) Hydration of nucleic acids components in dependence of nucleotide composition and relative humidity: a Monte Carlo simulation. Europ Phys J D
20(1):331–337
84. Shestopalova AV (2007) The binding of actinocin derivative with DNA fragments (Monte
Carlo simulation). Biopolym Cell 23(1):35–44
85. Auffinger P, Westhof E (1997) Molecular dynamics: simulations of nucleic acids. Rev
Comp Chem 11(2):317–328