Index
548
Complex prediction methodology, 373
Complexation,
actinocin derivatives, 29
molecular mechanisms of, 29
constants, 23
evaluation of, 23
cyclodextrine, 452
modeling of, 452
DNA-actinocin, 32
investigation of, 32
DNA-drug, 31
investigation of, 31
DNA-ligand, 30, 35, 46
energetics of, 46
investigation of, 30, 35
DNA-nucleic acid, 35
energetics of, 35
energetics of, 38, 39, 42
in carbohydrates, 283
in DNA, 23
in DNA-ligand system, 25
models of, 23
of water, 470
physical methods in, 24
weak, 274
Computational,
analysis, 28, 122
methods in, 28
approaches, 37, 114, 115, 124, 126, 185,
199, 209
binding energetics, 37
in DNA studies, 114
in enzyme-substrate interactions, 209
in Hazan et al’s study, 115
in pol inhibitor studies, 126
in polymerase studies, 126
in quantum chemical, 199
in quantum mechanics, 185
in rational design of DNA polymerase
inhibitors, 124
modeling, 117, 287, 543
of nanomaterials, 543
of protein ligand interactions, 117
studies, 173
techniques, 504
toxicology, 325–327, 336, 361
advantages of, 327
assessment of, 361
methods used in, 336
prediction of, 327, 361
significance of, 326
Computer,
modeling, 187, 196
of G-quadruplex structures, 187, 196
Computer-aided drug design, 502, 520
Conformational,
flexibility, 139, 146, 187, 199
in biological functions of DNA, 199
of DNA chains, 187
selection, 502, 507, 525
Conformational space, 16, 121, 164, 168, 174,
451, 507, 511, 517
Consensus approach, 372, 405, 412
Continuous molecular fields, 433, 434, 449,
452
advantages of, 453
and regression kernel-based machine
learning methods, 438
approach of, 434
in analyzing and visualizing chemical
databases and SAR/QSAR/QSPR
models, 441
in HIV reverse transcriptase (HIVRT), 448
in QSAR studies, 436
methods of, 435
trypsin inhibitors, 448
use of, 436
D
Density functional theory, 66, 68, 83, 189,
209, 210, 217
in gas phase, 73
in vitamin C study, 75
investigations using, 151
DFT See Density functional theory, 13
DNA,
damage, 60, 61, 78, 103
intercalator, 40, 47, 49
repair, 61, 78, 80, 81, 83
enzymatic, 78, 80, 81, 83
DNA dependent DNA polymerases (DNA
pols), 95
common pecularities of, 98, 99
diversity of, 96
Drug,
design, 22, 36, 39, 50, 182, 209, 218, 453,
502
discovery, 462, 503, 530, 540
E
Electrostatic potential surfaces (EPS), 209
Energy,
analysis, 43, 46–50
decomposition, 36, 37, 39–41, 118, 124
548
Complex prediction methodology, 373
Complexation,
actinocin derivatives, 29
molecular mechanisms of, 29
constants, 23
evaluation of, 23
cyclodextrine, 452
modeling of, 452
DNA-actinocin, 32
investigation of, 32
DNA-drug, 31
investigation of, 31
DNA-ligand, 30, 35, 46
energetics of, 46
investigation of, 30, 35
DNA-nucleic acid, 35
energetics of, 35
energetics of, 38, 39, 42
in carbohydrates, 283
in DNA, 23
in DNA-ligand system, 25
models of, 23
of water, 470
physical methods in, 24
weak, 274
Computational,
analysis, 28, 122
methods in, 28
approaches, 37, 114, 115, 124, 126, 185,
199, 209
binding energetics, 37
in DNA studies, 114
in enzyme-substrate interactions, 209
in Hazan et al’s study, 115
in pol inhibitor studies, 126
in polymerase studies, 126
in quantum chemical, 199
in quantum mechanics, 185
in rational design of DNA polymerase
inhibitors, 124
modeling, 117, 287, 543
of nanomaterials, 543
of protein ligand interactions, 117
studies, 173
techniques, 504
toxicology, 325–327, 336, 361
advantages of, 327
assessment of, 361
methods used in, 336
prediction of, 327, 361
significance of, 326
Computer,
modeling, 187, 196
of G-quadruplex structures, 187, 196
Computer-aided drug design, 502, 520
Conformational,
flexibility, 139, 146, 187, 199
in biological functions of DNA, 199
of DNA chains, 187
selection, 502, 507, 525
Conformational space, 16, 121, 164, 168, 174,
451, 507, 511, 517
Consensus approach, 372, 405, 412
Continuous molecular fields, 433, 434, 449,
452
advantages of, 453
and regression kernel-based machine
learning methods, 438
approach of, 434
in analyzing and visualizing chemical
databases and SAR/QSAR/QSPR
models, 441
in HIV reverse transcriptase (HIVRT), 448
in QSAR studies, 436
methods of, 435
trypsin inhibitors, 448
use of, 436
D
Density functional theory, 66, 68, 83, 189,
209, 210, 217
in gas phase, 73
in vitamin C study, 75
investigations using, 151
DFT See Density functional theory, 13
DNA,
damage, 60, 61, 78, 103
intercalator, 40, 47, 49
repair, 61, 78, 80, 81, 83
enzymatic, 78, 80, 81, 83
DNA dependent DNA polymerases (DNA
pols), 95
common pecularities of, 98, 99
diversity of, 96
Drug,
design, 22, 36, 39, 50, 182, 209, 218, 453,
502
discovery, 462, 503, 530, 540
E
Electrostatic potential surfaces (EPS), 209
Energy,
analysis, 43, 46–50
decomposition, 36, 37, 39–41, 118, 124