Computational Drug Discovery and Design

INDEX

A

Absorption, distribution, metabolism, excretion
and toxicity (ADMET)................................10–12,
71, 76, 127, 136, 272, 274, 275, 277, 278
Accuracy...................................................... 26, 27, 34, 38,
46, 126, 127, 132, 141, 147, 233, 234, 240, 327,
328, 334, 343, 349, 355, 371, 373, 380, 482
Acetaminophen...................................................246–247,
249, 250, 252, 253, 261
Acetycholinesterase ......................................................... 93
Aggregation..............................................v,298, 427–441
Alchemical transitions..........................................199–228
Allostery...................................................... 88, 93,97–99,
135, 138, 147, 286, 294, 340, 348, 352–355, 358
Area under the Curve (AUC)........................................ 27
Aryl acylamidase..................................................246–247,
249, 250, 252, 253, 261
Attribute-Relation File Format (ARFF) ..................23, 24
Attributes................................................................. 23, 26,
28, 99, 166, 190
Autodock................................................................. 33, 37,
40, 42, 43, 45, 47, 74, 76, 107, 149, 158, 162,
163, 369

B

Bcl-2 family ..................................................................... 99
Bcl-xL........................................................ 92, 93, 99, 123
Binding affinity..................................................74, 92, 95,
96, 106, 127, 135, 136, 147, 234, 235, 240, 242,
281, 286, 346, 355
Binding constant (Kd) .................................................... 34
Binding energy.........................................................32–34,
43, 73, 76, 106, 286
Binding free-energy...............................................v, 6, 81,
91, 136, 146, 147, 233, 235, 289, 368
Binding pocket...........................................106, 108–112,
114, 118, 119, 125, 127, 130, 132, 133, 146,
147, 235, 237, 392
Binding pockets............................................................... 92
Biological activity.................................................... 1, 2, 8,
32, 124, 125, 128, 132, 308–336
Biomolecular simulation software
AMBER.........................................................130, 153,
407, 414, 420, 446, 449
CHARMM .....................................................236, 414

GROMACS....................................... 74, 76,293, 399

NAMD.....................................................................414

ProtoMS ..................................................................210

Boltzmann-weighted Score (BS).........................108, 116

C

Carbonic anhydrase II.......................................7, 73, 124

CDK4.............................................................75,124, 291

Combinatorial chemistry ..............................................124

Computational medicinal chemistry........................ v, 278

Computational solvent mapping (CS-Map)............90, 98

Computer simulation...........................................147, 170

Conformational change .............................................7, 99,

100, 147, 222, 291, 296, 342–346, 348–355,

418, 456, 461, 465

Conformational ensemble...................................... 15, 33,

37, 88, 93, 94, 98, 413, 422

Conformational selection....................................147, 348

Conformational transition...................................339–358

Cryo-electron microscopy.............................36,146, 404

Curvature surface................................................234, 235,

237, 238, 240

Cyclic nucleotide phosphodiesterases..........................123

Cyclooxygenase-2 (Cox-2)..................................134–136

Cyscore........................................................233, 235, 237

D

Decoys...................................................16,117, 368, 369

Desolvation..........................................................6, 34, 46,

288, 289, 297, 300, 397, 398, 401

Diabetes mellitus...........................................................180

Differentially expressed genes......................................474

Disease.................................................................4, 22, 23,

38, 57, 66, 87, 93, 98, 180, 277, 278, 294, 428,

438, 474, 475, 482

Drug design.................................................. 1, 31, 51, 71,

100, 124, 145, 192, 272, 286, 350, 368, 390, 404

Drug development...............................................v, 11, 22,

28, 74, 97, 98, 123, 145, 271, 272, 279, 281,

404, 428

Drug discovery................................................v, vi, 2, 4, 8,

10–12, 21, 22, 31, 34, 36, 71, 72, 74, 123, 124,

129, 132, 135, 138, 140, 141, 145, 146, 233,

239, 346–356, 367

Druggability..........................................4, 87,89–97, 100

Mohini Gore and Umesh B. Jagtap (eds.),Computational Drug Discovery and Design, Methods in Molecular Biology, vol. 1762,
https://doi.org/10.1007/978-1-4939-7756-7,©Springer Science+Business Media, LLC, part of Springer Nature 2018

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