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https://t.me/med1917
Index
3D model 167
accuracy 227
Adaboost 197
ADME database 388–389
ADMET 182, 186, 198, 204
ADMET analysis 331, 336, 342
ADMET prediction 380, 382–383, 388,
392, 397
AdmetSAR 395
affinity 96, 98, 102, 111, 114, 123–124
algorithm 96, 101–102, 107–108, 112, 128
alignment 101–103, 111, 115
AMBER 157, 219, 221
Amprenavir 105, 125
analysis 94, 103–104, 106, 108, 110–120,
123–125, 128
analysis of packing 139
ANFIS 191, 205
angle bending 222
antibiotic 124–125
antifungal resistance 417
antiviral treatments 168
application 91, 105, 113, 117, 127
approach 91–93, 98, 102, 109, 114, 116, 118,
124–125
artificial intelligence 56–59
atorvastatin 124
atropisomer 86
AutoDock 72
AutoDock Vina 74
bagging and boosting GPR 197
Bat optimization algorithm 198, 205
BCR-ABL 411
beta-lactamases 410
binding affinities 151
binding affinity 213
binding free energy 212, 215
bioactivation 178
bioinformatic 118, 120
biological systems 154
biomolecular simulations 222
biomolecules 243, 245, 248, 259, 274–275, 277–279
biotransformation 175, 178–179, 203
Boltzmann factor 215
bond lengths and angles 138
boosted GPR 197
Born–Oppenheimer approximation 216
Broglie relationship 225
carboxy muconolactone decarboxylase 202
cardiovascular 100
case studies 28, 30, 33, 38
CCP4mg 140
central nervous system (CNS)-acting agents 420
CHARMM 154, 219
ChEMBLdb 393
chemical shift 330
cheminformatics 42
Chemistry at Harvard Macromolecular
Mechanics 220
ChimeraX 141
chiral 82
chirality 81
combinatorial 107, 113–115, 117
COMPASS force field 195
computational 91–93, 97, 99, 105–106, 110–113,
124, 127, 211
computational approach 226, 228
computational chemistry 151–152
computer 91, 93, 102, 107, 111, 116, 120, 123–124
computer-aided design 351
computer-aided drug design 133, 180, 204
computer-aided drug discovery 296
conformational 94, 96, 108, 112, 115–116, 125
consensus scoring 228
consensus scoring function 72
COOT (crystallographic object-oriented toolkit) 140
cosolvency 190
Coulombic potential energy 221
covalent bond 212
COVID-19 124–125, 152
COX 125, 128
CYP450 175, 177–178, 181, 184–187, 203–204
CypBoM 186
CypReact 181–182, 186, 203
CyProduct 186
cytochrome P450 175–176, 181, 183
database 96, 100, 102, 114
–116, 125
databases 51–55
https://doi.org/10.1515/9783111207117-017
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deep learning 183, 186–187, 195
deep neural network properties predictor 200,
202, 205
DeepTox 180
descriptor 105, 114
design 91–96, 98, 100, 105–108, 111–118, 120,
122–124, 126–128
designing target 151
development 91–93, 106, 111, 122–125, 127
DFT 81
diagnosis 91
Diamond 143
discovery 91–94, 100–101, 103, 109–111, 113, 116,
118–120, 122–123, 125, 127
disease 91–92, 94, 100, 119–120, 124
DNA gyrase 410, 419
DNA repair proteins 406
DOCK 74
docking 92–94, 96–100, 105–110, 112–113, 117–118,
123–125, 127
drug 91–96, 98, 100–103, 105–107, 109, 111–113,
115–116, 118–120, 122–128
drug design 23, 243–244, 246, 248–249, 252–253,
258, 262, 271, 274, 277
– clinical development 24
– hit generation 24
– lead discovery 24
– lead optimization 24
– post-marketing surveillance 25
– preclinical testing 24
– regulatory approval 24
– target identification and validation 24
Drug development 5
drug discovery 2, 4–5, 7, 10, 12–13, 15–17, 19
–20,
228, 237, 243, 246, 248, 252, 261–262, 269,
271–273, 275–279, 320
drug resistance 243, 252, 254–257, 259, 277
drug solubility 175, 198, 200
DrugBank 392–393
drug-drug interactions 176, 182, 184, 186
DSSTox 388–389
dynamic 94, 96, 98, 123
dynamic behavior 151
dynamics simulations 227
effectiveness 124
efflux pumps 404, 406
EGFR or BRAF mutations 406
electron density maps 139
electronic polarization 212
empirical scoring 226
empirical scoring functions 71
energy perturbation 229
enthalpy 214
entropy 214
enzyme 100, 112, 123–124, 127
epidermal growth factor receptor 411
equilibrium constant 215
equilibrium dissociation 216
Erwin Schrödinger 223
extended-spectrum beta-lactamases 410
Famotidine 125
fast shape matching algorithm 68
FlexX 75
force field 228
force field and initial configuration 232
force field scoring 227
force-field-based scoring functions 71
formulation 92
Fourier transform infrared spectroscopy 325
fragment-based drug design (FBDD) 32
Gaussian process regression 197, 205
GCNN 187, 204
General Force Field 157
general rule from the delivery perspective 176
generalized Born surface area 231
genetic algorithm 69
genomics 243, 245–246, 248–250, 252–254,
259–262, 267–269, 271–275,
277–279
Gibbs free energy 213
Gibbs free energy equation 216
glaucoma 124–125
Glide 75, 111, 113, 118
GOLD 74
harmonic oscillator model 217
Hermitian operator 226
high-throughput screening 307, 356
high-throughput screening (HTS) 7, 27
hit-to-lead 212
HIV 105–106, 124–128
430 Index
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homology 102, 111, 114–115, 117–118, 125
HTS 212
hydrogen bonding 139
hyphenated techniques 322, 327, 332, 336–337
identification 91, 93–94, 98, 102–103, 117, 119,
124–125
in silico 212
incremental construction algorithm 69
infection 106, 125, 128
influenza 124, 126–127
interaction 93, 96, 99–100, 108–109, 112, 116–117,
123, 246, 270
intermolecular interactions 139
intramolecular rotation 219
isoniazid 125
isothermal–isobaric 232
JANA2006 143
J-ICE 144
Jmol 140
kelvin 216
kernel ridge regression 198
knowledge-based scoring 228
knowledge-based scoring functions 71
Lazar 394–395
LBDD 5, 11, 18–19
lead 91–94, 100, 103, 107, 113–115, 117, 122, 211
lead-hit-based methods 26
leave-one-out cross-validation 183
Lennard–Jones potential 221
ligand 51–56, 60, 92–94, 96, 98–100, 102, 106–109,
111–114, 116, 118, 123, 125
ligand-based drug design 5, 296
ligand-based drug design (LBDD) 134
ligand-based methods 384
ligand–protein complex 228
ligand–protein complexes 228
ligand–protein interactions 228, 236
linear solvation energy relationship 189, 204
machine 120
machine learning 175, 180, 204
macromolecules 352
Markov chain Monte Carlo 234
MD simulations 154
mechanics/molecular mechanics 236
Merck molecular force field 220
Mercury 142
MetaboGen 186, 204
metadynamics 151, 236
methicillin-resistant Staphylococcus aureus 410
MM2 219
MM3 219
MM4 219
MM-GBSA 231
MMPBSA 234
modeling 92–94, 100–103, 105–107, 109–110,
112–114, 116–118, 122–125, 127
modified Wilson model 190
modified Wilson’s models 196
molecular docking 86, 226, 340
molecular dynamic (MD) simulation 8
molecular dynamics 84, 222, 307
molecular mechanics 216, 233
molecular mechanics Poisson–
Boltzmann surface
area 234
molecular mechanics-generalized Born surface
area 231
molecular modeling 7, 219, 382–384
molecular recognizable tools 133
molecular systems 152
Monte Carlo 70, 233
MRSA infections 366
multilayer perceptron 198
multi-layer perceptron neural network 205
multilayer perceptron neural network 195
Mycobacterium tuberculosis 418
natural product screening 39
natural product-derived compounds 40
neural network 304
nonbonded interactions 228
norfloxacin 105, 125
OPLS 222
optimization 51–52, 92–94, 96, 103, 107, 111,
114–115, 117, 119, 244, 250–252, 254, 259, 262,
267, 270, 274, 276–278
optimized potentials for liquid simulations 222
out of the plane 220
parameterization 213
penicillin-binding proteins 410
Index 431
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peptidic ligands 353
peptoids 372
pharmacophore 92, 100–102, 108, 113–114, 117,
124–125, 127, 339
pharmacophore modeling 384
Pharmacophore models 12
PHENIX 143
phenotypic screening 36
Poisson–Boltzmann 235
potential energy 227
PPI modulators 358
preclinical 92
prediction 100, 103, 105, 110–112, 116, 118–119, 125
prediction of molecular properties 176
protein 53, 93–94, 96, 98, 100, 102, 105–117, 119,
123–125, 127
PubChem 392–393
PyMOL 139
QSAR 43, 82, 101, 103–104, 113, 117–118, 213
QSAR (quantitative structure–activity
relationship) 2
quality 58
quantitative structure property relationships
189, 205
quantum 94, 104, 106, 110, 112, 116, 211
quantum effects 211
quantum mechanical 212
quantum mechanics 223, 233
quantum mechanics/molecular mechanics
(QM/MM) 152
receptor 96–100, 106–108, 111–114, 117–118, 123,
125–126
regression 103, 116, 120
relationship between logP (lipophilicity) and SR in
water-based solvents 189
replica exchange MD 151
research 92, 109–112, 114
RMSF 170
RNA 117, 124
SARS 124–125
SBDD 5, 10–11, 14, 17–19, 92–94, 98, 100, 105–106,
125, 128
scaffold 114
Schrödinger equation 223
scoring 93, 97–98, 100, 102, 107–108, 110, 114, 117
scoring functions 71
semi-empirical 228
semiempirical quantum mechanical 213
semiempirical scoring 227
SHELX 143
simulated annealing 70
software 93–94, 103, 105–106, 109–113, 115–118, 123
solubility 175–176, 203
solvent effects 139
solvent-accessible surface area 235
spectroscopic techniques 320–324, 332, 336, 343
squantum effects 236
statistical analyses 228
stereocenters 83
stereochemical parameters 139
stereochemistry 81
stereoisomer 89
stretching 218
structural databases 228
structure based drug design 307
structure-based 383–384
structure-based drug design 340
structure-based drug design (SBDD) 134
subatomic 216
SwissADME 394–
395
Tabu search 70
target 92–94, 96–98, 100, 102, 105–106, 111, 113,
115, 118–119, 124, 127, 243–244, 247–248,
250–252, 254, 257–259, 261–262, 269, 271,
273–274, 276–279
target-based mechanisms 406
therapeutic 91–92
time-dependent Schrödinger 225
time-dependent Schrödinger equation 224
ToxBank 389
toxicity 177, 180, 204
Toxtree 394
UNIQUAC model 196
Validation 55, 92, 103
validation of force fields 151
Van der Waals 220, 222
432 Index
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Van’t Hoff equation 216
vascular endothelial growth factor 412
VESTA 142
virtual 51–56, 59–61, 92, 94, 96, 98, 100–101, 107,
111, 113–115, 119, 125, 127–128
virtual screening 29, 87
VMD 140
VTNMR 81
Werner Heisenberg 223
XP docking 230
X-ray crystallography 133, 152, 308
XtalDraw 142
XtalView 143
ΔG 213
β-tubulin 414
Index 433
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