R
Ramachandran plot, 117, 118, 182, 391
Receptor-based pharmacophore, 35, 47
Receptor-ligand binding, 115
Reliable predictions, 3
Residue interaction network, 16, 55–58, 282
Ribonucleic acid, 189, 234, 243, 248, 250, 311,
325, 335, 358
Ribosomal unit, 326, 330
Rifampicin, 309, 311, 322, 330
RmlC, 314, 325
RNA polymerase enzyme, 322
Root mean square deviation, 30, 117
rpoB, 322, 335
S
Sampling algorithms, 6
Sampling efficiency, 5
Scaffold hopping, 48, 71, 73, 74, 107, 208, 259
Scaffolds, 40, 45, 46, 75, 109, 110, 256, 257,
260–262, 276, 288, 324
SecA, 320
Signal transduction, 56, 61, 62, 180, 318, 325,
367
Simplified molecular-input line-entry system,
85, 87, 89, 256
Solute-solvent interactions, 8
Solvation effects, 8, 9
Solvation energy, 8, 158, 238, 285
Solvation free energies, 8, 158, 227
Sorafenib, 113
Specificity, 30, 31, 36, 61, 113, 130, 134, 147,
179, 222, 223, 231, 275, 286, 288, 293,
322
20S proteasome, 323, 325, 393
Stacking interaction, 184, 186, 201, 207
Staphylococcus aureus, 315, 316
Statistical mechanics, 11
Steric environment, 28
Streptomycin, 75, 98, 99, 309, 311
Structural biology, 130, 230, 273, 295, 313,
323, 356, 371, 375, 376
Structure-based, 3, 4, 32, 35, 37, 38, 41, 43, 45,
109, 150, 213, 235, 261, 262, 271, 273,
287, 290, 307, 314, 315, 317–320, 323,
324, 336
Substrate binding, 2, 4, 5, 15, 17, 41, 133, 136,
188, 195
Substrate envelope hypothesis, 2
Substructure, 35, 73–75, 199, 256, 257, 286
Sunitinib, 113
Surface plasma resonance, 286
Sutezolid, 333, 334
Synergy, 250
Systems biology, 110, 113, 350
T
Tanimoto, 260, 289
Target site mutations, 2
Tautomeric, 28
Taxonomy, 119, 120
TBI-223, 333, 334
Tertiary structure, 3, 180
Test sets, 3, 95, 213
Thermodynamic integration, 11, 13, 110
Thermodynamics of protein-ligand binding, 6,
7
Thioredoxin reductase, 185, 332, 335
Topological biophore, 77
Topological parameters, 55, 59
Toxicity prediction, 25, 48, 230, 257
Toxicophores, 145, 160
Training sets, 35, 61, 71, 75–78, 91, 92, 94–96,
210, 212, 213, 287
Transmembrane receptor, 159
Tuberculosis, 3, 27, 75, 90, 98, 119, 282, 307,
309, 326, 334
Tyrosine phosphatase A, 318
Tyrosine phosphatase B, 318
U
Universal gas constant, 6
V
Vaccine, 179, 273, 333, 371
Van der Waals, 6, 9–11, 30, 42, 58, 124, 130,
147, 152, 158, 203, 207, 210, 228, 233,
237, 280, 290
Vertex, 56, 71, 74–82, 86, 87, 89, 90, 92, 94,
97–100, 102, 107
Vertex index, 71, 74, 76, 77, 79, 92
Vertex symmetry, 86
Virtual screening, 11, 25–27, 32, 41, 43, 44,
48, 144, 145, 182, 207, 214, 230, 234,
235, 258, 259, 262, 263, 285, 318, 320,
323, 330, 362
W
WHAT IF, 121
X
X-ray, 5, 30, 37, 116, 117, 141, 182, 195, 199,
205, 206, 210, 213, 215, 261–263,
272–275, 286, 313, 319, 321–324, 330,
376, 377, 379, 384, 389, 390
Z
ZINC database, 146
406
Index
Ramachandran plot, 117, 118, 182, 391
Receptor-based pharmacophore, 35, 47
Receptor-ligand binding, 115
Reliable predictions, 3
Residue interaction network, 16, 55–58, 282
Ribonucleic acid, 189, 234, 243, 248, 250, 311,
325, 335, 358
Ribosomal unit, 326, 330
Rifampicin, 309, 311, 322, 330
RmlC, 314, 325
RNA polymerase enzyme, 322
Root mean square deviation, 30, 117
rpoB, 322, 335
S
Sampling algorithms, 6
Sampling efficiency, 5
Scaffold hopping, 48, 71, 73, 74, 107, 208, 259
Scaffolds, 40, 45, 46, 75, 109, 110, 256, 257,
260–262, 276, 288, 324
SecA, 320
Signal transduction, 56, 61, 62, 180, 318, 325,
367
Simplified molecular-input line-entry system,
85, 87, 89, 256
Solute-solvent interactions, 8
Solvation effects, 8, 9
Solvation energy, 8, 158, 238, 285
Solvation free energies, 8, 158, 227
Sorafenib, 113
Specificity, 30, 31, 36, 61, 113, 130, 134, 147,
179, 222, 223, 231, 275, 286, 288, 293,
322
20S proteasome, 323, 325, 393
Stacking interaction, 184, 186, 201, 207
Staphylococcus aureus, 315, 316
Statistical mechanics, 11
Steric environment, 28
Streptomycin, 75, 98, 99, 309, 311
Structural biology, 130, 230, 273, 295, 313,
323, 356, 371, 375, 376
Structure-based, 3, 4, 32, 35, 37, 38, 41, 43, 45,
109, 150, 213, 235, 261, 262, 271, 273,
287, 290, 307, 314, 315, 317–320, 323,
324, 336
Substrate binding, 2, 4, 5, 15, 17, 41, 133, 136,
188, 195
Substrate envelope hypothesis, 2
Substructure, 35, 73–75, 199, 256, 257, 286
Sunitinib, 113
Surface plasma resonance, 286
Sutezolid, 333, 334
Synergy, 250
Systems biology, 110, 113, 350
T
Tanimoto, 260, 289
Target site mutations, 2
Tautomeric, 28
Taxonomy, 119, 120
TBI-223, 333, 334
Tertiary structure, 3, 180
Test sets, 3, 95, 213
Thermodynamic integration, 11, 13, 110
Thermodynamics of protein-ligand binding, 6,
7
Thioredoxin reductase, 185, 332, 335
Topological biophore, 77
Topological parameters, 55, 59
Toxicity prediction, 25, 48, 230, 257
Toxicophores, 145, 160
Training sets, 35, 61, 71, 75–78, 91, 92, 94–96,
210, 212, 213, 287
Transmembrane receptor, 159
Tuberculosis, 3, 27, 75, 90, 98, 119, 282, 307,
309, 326, 334
Tyrosine phosphatase A, 318
Tyrosine phosphatase B, 318
U
Universal gas constant, 6
V
Vaccine, 179, 273, 333, 371
Van der Waals, 6, 9–11, 30, 42, 58, 124, 130,
147, 152, 158, 203, 207, 210, 228, 233,
237, 280, 290
Vertex, 56, 71, 74–82, 86, 87, 89, 90, 92, 94,
97–100, 102, 107
Vertex index, 71, 74, 76, 77, 79, 92
Vertex symmetry, 86
Virtual screening, 11, 25–27, 32, 41, 43, 44,
48, 144, 145, 182, 207, 214, 230, 234,
235, 258, 259, 262, 263, 285, 318, 320,
323, 330, 362
W
WHAT IF, 121
X
X-ray, 5, 30, 37, 116, 117, 141, 182, 195, 199,
205, 206, 210, 213, 215, 261–263,
272–275, 286, 313, 319, 321–324, 330,
376, 377, 379, 384, 389, 390
Z
ZINC database, 146
406
Index
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