Computational Drug Discovery and Design

Modulators..................................................286, 299, 430
Molecular docking ........................................................v, 5,
31–48, 71, 74, 76, 79, 90, 127, 239, 273, 308,
367–386, 445–451
Molecular dynamics (MD)............................................88,
93–96, 98–101, 147–150, 152–154, 156–159,
162, 165–167, 169, 170, 173, 299, 300, 341,
342, 345–351, 354–356, 358, 394, 395, 397,
399, 400, 405, 407, 408, 422, 446–448, 451–453
Molecular flexibility....................................148, 368, 369
Molecular modeling................................32, 37,146, 392
Monte Carlo (MC) .........................................6,135, 194,
288, 297, 342, 343, 420
Mycobacterium tuberculosis...........................................292

N

Neuraminidase.......................................97,369, 371–373
NMR spectroscopy.........................................36,404, 449
Nuclear magnetic resonance (NMR)..................... 15, 36,
93, 145, 149, 150, 173, 281, 343, 348–350, 353,
354, 358, 371, 404, 431, 438, 449

P

Pairwise correlation.......................................................354
Pancreaticβ-cells...........................................................180
Pharmacokinetics...................................................v, 1, 11,
12, 47, 76, 124, 132, 136, 271–282
Pharmacophore...................................................8, 10, 12,
15, 79, 106, 127, 128, 130, 272, 294, 348
Phylogeny........................................................................ 54
p38 MAP kinase...................................................123, 421
Principal component analysis (PCA).................... 94,293,
413–415
Protein data bank (PDB)........................................ 36, 73,
91, 108, 130, 149, 234, 273, 296, 367, 396, 414,
431, 445
Protein flexibility..................................................... 34, 92,
93, 95, 100, 146, 299, 404
Protein–ligand binding........................................... 23, 74,
234, 235, 239, 389, 398
Protein–ligand docking................... v,105–119, 233–242
Protein–ligand interaction....................................... v,135,
166, 242, 389, 396, 401, 404
Protein–protein docking (PPD)..............v,107, 285–300
Protein–protein interactions (PPIs)....................... 89, 90,
285–288, 299, 348, 356, 429, 437
Protonation site.............................................................392

Q

Quantitive Structure Activity Relationship
(QSAR)......................................6,10–12, 78, 309
Quantum mechanics (QM)................................147, 342,
356, 401, 418, 421

R

Random forest.....................................................310, 321,

324, 329–331, 334

RNA....................................................................... 66,182,

194, 339, 474, 475

Root mean square deviation (RMSD)................. 44,148,

159, 160, 167, 234, 235, 296, 300, 369, 370,

376, 378, 380, 418, 423, 434, 435, 441, 447,

450, 453

S

Scaffold hopping ..........................................................6, 8,

74, 76, 125

Scoring function....................................................... v, 5, 6,

34, 37, 43, 80, 116, 117, 124, 127, 128, 132,

134, 147, 174, 233–235, 287, 288, 296, 298,

299, 368, 369, 373, 377, 378

Sensitivity........................................................27,180, 480

Solvation................................................................ 81,131,

166, 287, 343, 350, 418

Specificity................................................................. 27, 87,

126, 136, 138, 170, 367, 369, 480

Structure-based drug design (SBDD) ..........................31,

32, 47, 100, 368, 389, 404

Structure-based virtual screening (SBVS)....................31,

105, 106

T

Therapeutic Target Database (TTD)............................. 23

Thermodynamic integration (TI).......................205, 215

Thermodynamics........................................................ v, 97,

234, 295, 347, 348, 369, 389–401, 404, 405,

421, 422

Three-dimensional Zernike descriptors

(3DZD).................106, 109, 111, 112, 114, 115

TNF-alpha .....................................................................135

Toxicity.................................................................v,10–12,

71, 73, 127, 271, 272, 275

Transmembrane proteins...............................................98,

290, 291, 293, 295–298, 300, 405

Tyrosine kinase.................................................73–76, 347

U

Urokinase.......................................................................123

V

Vascular endothelial growth factor receptor-2

(VEGFR-2).............................................73, 74, 76

Virtual screening (VS)..................................................v, 2,

31, 71, 105, 108, 116, 117, 148, 149, 158,

162–166, 234, 291, 308, 309, 311, 312, 329,

348, 354, 368

COMPUTATIONALDRUGDISCOVERY ANDDESIGN

Index^487