E
Elastic network model (ENM)...........288, 343, 349, 357
Energy minimization.............................................. 15, 81,
129, 152, 153, 166, 167, 288, 449, 451
ENTREZ..............................................................190, 192
Estrogen................................................................. 73, 114
F
Force field................................................................ 34, 78,
100, 127, 129, 132, 147, 151, 162, 170, 236,
287, 342, 349, 356, 391, 394, 400, 446, 452
Fragment-based mapping algorithm
(FTMAP)................................................90–92, 98
Free energy..........................................................5, 34, 81,
91, 136, 146, 233, 289, 341, 397, 405, 416
Free energy perturbation (FEP)..................................... 94
G
Generalized AMBER Force Field (GAFF).........162, 408
Genetic algorithms (GAs)............................................... 33
Gibbs free energy (ΔGL)................................................. 34
Glycosaminoglycans (GAGs)......................445, 450, 453
G-protein coupled receptors (GPCRs).........................98,
290, 293–298, 308, 310–313, 348, 351, 353, 355
Graphic user interface (GUI)............................... 22,107,
150, 162, 173
H
H5N1.............................................................................. 98
Heat shock protein 90 N-terminal domain
(Hsp90)...................................................... 95, 123
Hepatitis C virus (HCV) ..............................................138
High-throughput screening (HTS)..................5, 10, 124
Hit prioritization............................................... 2, 3,8–11,
35, 58, 59, 63–66, 92, 125, 145, 172, 174,
276–278, 382
HIV integrase.................................................................. 93
HIV protease.......................................................... 75, 124
HIV-1 protease (HIVpr) ......................97,390, 396–398
Hot spot..................................................... 87, 88, 91, 95,
96, 98–100, 156, 281, 286, 373, 427
Hydration site........................................................ 97,391,
394–398, 446
I
Insulin...................................................................180, 474
L
Lead identification ..............................................124, 125,
133–136, 242, 278, 347, 398, 401
Lead optimization.......................................124, 401, 404
Ligand-based virtual screening (LBVS).......................105
Lipinski’s rule of-five..........................................2, 11, 76,
116, 127, 136, 158
Logistic regression..............................324, 326–329, 335
Lowest conformation score (LCS)...............................108M
Machine learning...................................................6–8, 12,
15, 16, 21–28, 52, 63, 99, 308–311, 313–315,
320, 322, 323, 326, 327, 331–335, 368
Major histocompatibility complex proteins
(MHC)...............................................................292
Matthews Correlation Coefficient
(MCC)................................................................. 27
Microarray .................................v, 21,179–194, 479, 482
MicroRNA............................................................473–483
Modeling software and algorithm
AGGRESCAN................................................429, 438
ATTRACT.............................................288, 289, 291
AutoDock...........................................................33, 37,
40, 42, 43, 47, 74, 76, 107, 149, 158, 162, 163
BLAST................................................................53–55,
57, 59, 62, 65, 67
ChemAxon’s Standardizer........................................ 14
Cyscore....................................................................233
Cytoscape...............................................181, 190, 192
DOCK......................................................33,286, 297
FRODOCK...........................................288, 289, 291
FTDock....................................................................288
FTMAP.........................................................90–92, 98
GRAMM................................................288, 289, 296
HADDOCK..................................289, 292, 293, 296
KNIME................................................................22, 23
LigBuilder....................................................73, 74, 77,
129, 130, 132, 133, 135, 141
MacroModel............................................................129
MODELLER...........................................62,135, 149
MolFit.............................................................288, 289
OMEGA ...............................106, 108–110, 312, 332
Open Babel..................................................37, 39, 47,
108–110, 273, 451
PIPER....................................................288, 289, 291
pkCSM....................................................272–278, 281
PL-PatchSurfer...............................................108, 113
PROFEAT................................................................. 23
PseAAC-Builder ........................................................ 23
QikProp.................................. 81,129, 132, 136, 141
R software................................................................182
RapidMiner..........................................................22, 23
Scikit-learn...............................................22,311, 321,
322, 324, 331, 333
UCSF Chimera.................................... 37, 39, 42, 109
WEKA........................................................................ 22
ZDOCK.........................................288, 289, 292, 296
ZINC............................. 36,110, 116, 119, 158, 278486
COMPUTATIONALDRUGDISCOVERY ANDDESIGN
Index