226–228, 233, 237, 238, 277, 280, 281,
283–285, 290, 315, 316, 360
EmbB, 313, 314
Empirical scoring functions, 3, 4, 138
Enrichment, 4, 140, 147, 260
Enthalpy, 6, 110, 114, 115, 133, 137, 152, 154,
155, 157
Entropy, 6, 7, 9, 16, 110, 114, 115, 133, 137,
138, 152, 154–157, 263, 276
E-pharmacophore, 38, 40–43
Epigenetic, 247, 248, 250, 251, 255–264
Epitopes, 122
Ethambutol, 309, 311, 314, 330
Explicit solvent, 8, 9, 123, 125, 227
Extensively drug resistant, 307
F
Filamenting temperature-sensitive protein Z,
322
Fitness cost, 2, 15, 17, 18
Flavin, 183, 316
Flavone, 294
Flexible docking, 11, 290, 291, 294
Fluoroquinolone, 321, 330
Fluvastatin, 115
Flux balance analysis, 113
Food and Drug Administration (FDA), 17, 45,
112, 115, 128, 146, 230, 248, 251, 255,
286, 288, 320, 326, 330, 332, 336, 350,
366, 367
Force fields, 5, 9, 10, 39, 144, 149, 153, 226,
230, 231, 234, 259, 279–281, 283, 290,
350, 356
Fragment-based drug design, 25, 48, 260, 264
Framework, 27, 30, 45, 46, 48, 74, 256,
352–356, 360, 370, 385
Free energy, 2–9, 11–13, 15–18, 109, 114, 115,
125, 128, 133, 137–139, 150–152, 155,
157–159, 161, 221, 224, 225, 227, 228,
231, 239, 243, 272, 276, 283, 290, 294,
358
Free energy perturbation, 6, 11–13, 109, 159,
272
Fumaratehydratase, 320, 325
G
Gatifloxacin, 311, 326, 330
Genetic algorithm, 34, 110, 137, 144, 150, 211,
213, 278
Genomic wide association, 112
Gibbs equation, 6
Gibbs free energy, 6, 137, 138, 224
Glide, 38, 41, 44, 139, 143, 144, 153–155, 207,
214, 234, 278, 291, 292
Glutaminesynthetase, 320
Glycoprotein, 224, 225
G protein-coupled receptor, 62, 273
Gram-negative, 330
Gram-positive, 315, 327, 330
Graph theory, 56, 57, 73, 106
Grid computing, 5
GSK070, 332
GSK693, 314
H
Hadoop, 352–358, 360, 363, 370
Hemagglutinin, 122
Heterogeneity, 43, 85, 370, 384, 391, 392
Hexadecahydro-1 h-cyclopenta[a]
phenanthrene framework, 45
High-Performance Computing (HPC), 348,
350, 356, 363, 366
High-resolution, 3, 375–377, 379–381, 383,
384, 387–389, 391
High-throughput virtual screening, 11, 362
HipHop, 32–34, 287
Histone, 186, 187, 247–252, 255
Homodimeric, 119
Homology model, 116, 120, 182–184, 187,
261, 262, 318
Human immunodeficiency virus, 232
Human serum albumin, 122, 123
H56 vaccine, 333
Hybridization state, 37
Hydrogen bonds, 6, 37, 59, 86, 115, 159, 181,
184, 188, 272
Hydrophilic, 60, 61, 188, 207, 208
Hydrophobic, 10, 28–30, 34, 36, 38, 41, 45, 56,
58, 60, 61, 113, 114, 122, 137, 139, 159,
179–182, 184–188, 197, 199, 201–203,
205–208, 210–213, 215, 261, 284, 293,
319, 322
Hypermethylation, 249
Hypogen, 32–34, 213, 214, 287
Hypomethylation, 249
I
Imipenem, 326, 328
Immunosuppression, 190
Implicit solvent, 8, 227
Inactive range value, 80
Indinavir, 115
Induced fit, 115, 125, 135, 144, 272, 291, 292
Induced fit docking, 144, 272, 291, 292
Index
403
283–285, 290, 315, 316, 360
EmbB, 313, 314
Empirical scoring functions, 3, 4, 138
Enrichment, 4, 140, 147, 260
Enthalpy, 6, 110, 114, 115, 133, 137, 152, 154,
155, 157
Entropy, 6, 7, 9, 16, 110, 114, 115, 133, 137,
138, 152, 154–157, 263, 276
E-pharmacophore, 38, 40–43
Epigenetic, 247, 248, 250, 251, 255–264
Epitopes, 122
Ethambutol, 309, 311, 314, 330
Explicit solvent, 8, 9, 123, 125, 227
Extensively drug resistant, 307
F
Filamenting temperature-sensitive protein Z,
322
Fitness cost, 2, 15, 17, 18
Flavin, 183, 316
Flavone, 294
Flexible docking, 11, 290, 291, 294
Fluoroquinolone, 321, 330
Fluvastatin, 115
Flux balance analysis, 113
Food and Drug Administration (FDA), 17, 45,
112, 115, 128, 146, 230, 248, 251, 255,
286, 288, 320, 326, 330, 332, 336, 350,
366, 367
Force fields, 5, 9, 10, 39, 144, 149, 153, 226,
230, 231, 234, 259, 279–281, 283, 290,
350, 356
Fragment-based drug design, 25, 48, 260, 264
Framework, 27, 30, 45, 46, 48, 74, 256,
352–356, 360, 370, 385
Free energy, 2–9, 11–13, 15–18, 109, 114, 115,
125, 128, 133, 137–139, 150–152, 155,
157–159, 161, 221, 224, 225, 227, 228,
231, 239, 243, 272, 276, 283, 290, 294,
358
Free energy perturbation, 6, 11–13, 109, 159,
272
Fumaratehydratase, 320, 325
G
Gatifloxacin, 311, 326, 330
Genetic algorithm, 34, 110, 137, 144, 150, 211,
213, 278
Genomic wide association, 112
Gibbs equation, 6
Gibbs free energy, 6, 137, 138, 224
Glide, 38, 41, 44, 139, 143, 144, 153–155, 207,
214, 234, 278, 291, 292
Glutaminesynthetase, 320
Glycoprotein, 224, 225
G protein-coupled receptor, 62, 273
Gram-negative, 330
Gram-positive, 315, 327, 330
Graph theory, 56, 57, 73, 106
Grid computing, 5
GSK070, 332
GSK693, 314
H
Hadoop, 352–358, 360, 363, 370
Hemagglutinin, 122
Heterogeneity, 43, 85, 370, 384, 391, 392
Hexadecahydro-1 h-cyclopenta[a]
phenanthrene framework, 45
High-Performance Computing (HPC), 348,
350, 356, 363, 366
High-resolution, 3, 375–377, 379–381, 383,
384, 387–389, 391
High-throughput virtual screening, 11, 362
HipHop, 32–34, 287
Histone, 186, 187, 247–252, 255
Homodimeric, 119
Homology model, 116, 120, 182–184, 187,
261, 262, 318
Human immunodeficiency virus, 232
Human serum albumin, 122, 123
H56 vaccine, 333
Hybridization state, 37
Hydrogen bonds, 6, 37, 59, 86, 115, 159, 181,
184, 188, 272
Hydrophilic, 60, 61, 188, 207, 208
Hydrophobic, 10, 28–30, 34, 36, 38, 41, 45, 56,
58, 60, 61, 113, 114, 122, 137, 139, 159,
179–182, 184–188, 197, 199, 201–203,
205–208, 210–213, 215, 261, 284, 293,
319, 322
Hypermethylation, 249
Hypogen, 32–34, 213, 214, 287
Hypomethylation, 249
I
Imipenem, 326, 328
Immunosuppression, 190
Implicit solvent, 8, 227
Inactive range value, 80
Indinavir, 115
Induced fit, 115, 125, 135, 144, 272, 291, 292
Induced fit docking, 144, 272, 291, 292
Index
403