REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 11 (1997)

The numbers following each term refer to the pages on which it is mentioned. Computer programs are denoted in boldface; databases and journals are in italics. (This document does not contain the minor corrections that were made to the proofs.)

Return to the RCC Table of Contents
Return to the RCC Indexes
Return to "Reviews in Computational Chemistry" home page


Ab initio calculations, 145
ACE inhibitors, 105
Acid proteinase inhibitor, 105
Aconitase, 47
Acrobat, 387
Active analog approach (AAA), 143, 187
Active site, 1, 2, 23, 29, 31, 50, 68, 77, 84, 188
Adamantane, 108
Adenylate kinase, 105
Advanced Research Projects Agency Network (ARPAnet), 374
Aggregation, 252
Agonist, 2
ALADDIN
, 36, 143
Alignment, 135, 141, 144, 169, 184, 186, 226
Alkanes, 245
ALOGP
, 268, 295, 301
AltaVista
, 378, 379
AM1, 145, 222, 279
AMBER
, 71, 81, 88, 321, 328, 330, 345, 348, 354, 355, 356, 357, 358, 359, 361, 363, 387, 390, 396
American Association for the Advancement of Science, 384
American Chemical Society, 384
American Crystallographic Association, 384
p
-Amidinophenylpyruvate (APPA), 24, 43
Amidinothiophene, 7
Amino acids, 39, 249, 254, 260, 263, 268, 269
AMP, 105
Ampicillin, 273
Androgen receptor binding, 34
Angiotensin-converting enzyme (ACE), 34, 149
Antagonist, 2
Antiparasitic agent, 45, 111
Antiviral ribonucleoside, 204
APEX-3D
, 139, 387
Aromatase inhibition, 160
Aromatic system, 247, 263
Artificial intelligence (AI), 24, 35, 151, 265
Aspartyl protease, 39
Assumptions in 3D QSAR, 135
Atom-based approach, 75
Atomic charge, 145, 188, 280
Atropine, 293
Autocorrelation, 220
AUTODOCK
, 15, 16, 44, 47
Available Chemicals Directory
, 10, 45

BABEL
, 103
Back-propagation, 193
Base pair geometry, 321
Basis set STO-3G, 222, 277
Batch mode, 102
BEELINE algorithm, 25
Beilstein
, 56
Bending Dials
, 348
Benzamidine, 23
Benzene, 292
Benzene sulfonamides, 223
Benzodiazepine, 105, 149
Benzoic acids, 168, 222, 253
Benzoquinones, 45
Betamethasone, 281
Binding, 98, 99, 106, 159, 188, 195, 300
Binding affinity, 86, 87, 88, 89, 90, 95, 97, 113, 128, 141, 171, 223
Binding energies, 91, 101, 130, 136, 224
Binding sites, 72, 94, 135, 203, 207, 226
Bioactive conformation, 47, 135, 142, 144, 186, 188, 195, 199, 302
Bioassays, 141
Bioavailability, vi, 92, 97, 113, 128, 171, 195
Biodistribution, 286
Bioisoteric replacement, 141
Biological activity, 170, 171, 184, 204
Biological drift, 130
Biological membranes, 296
Bionet, 380
Biophores, 140
BIOSYM tool control language (BTCL), 104
Biphenyl, 255
Birkbeck College, 381
Bis(p-chlorophenoxy)hexane, 279
BLOGP
, 279, 295, 297, 302
Boltzmann statistics, 142
Bootstrapping, 154, 156, 169
Brainstorming, 102, 112
Brevotoxin b, 46
Bridging groups, 7, 23, 29
Brookhaven National Laboratory, 384
Brookhaven Protein Data Bank
, 103, 325, 380, 396
Browser, ix, 376
Brute force methods, 24
BUCKETS
, 5, 18, 22
BUILDER
, 102
Building blocks, 17, 23, 40, 41, 50, 51
Building strategies, 76, 112
Buildup procedure, 39

CAChe
, 396
CADPAC
, 387
CAESA
, 44, 92, 94
Cambridge Crystallographic Data Centre, 380
Cambridge Structural Database (CSD)
, 3, 6, 7, 9, 10, 22, 23, 24, 29, 46, 72
Cambridge University, 382
CambridgeSoft Corporation, 387
cAMP, 105
Canonical ensemble, 331, 332, 355, 362
Capacity factors, 242
Carbo similarity index, 213
Carbonic anhydrase, 105, 223
Carboxypeptidase A, 40
Casting, 46
Cathepsin-L, 46
CAVEAT
, 9, 10, 22, 24, 28, 68
CAVITY
, 31
Cavity formation, 246
Central box, 332, 334
Cerius[2] MFA
, 139, 389, 396
CGCGAATTCGCG dodecamer, 327, 328, 342, 349, 359, 361, 362
Chain closure algorithm, 25
Chameleon effect, 252, 298
Chance correlation, 134, 139, 154, 185, 194, 199, 202, 226
Charge distribution, 270, 280
Charge groups, 363
Charge transfer, 149, 243, 247
Charged cylinder, 321
CHARMM
, 20, 94, 218, 323, 330, 361, 387, 396
Chem3D
, 387
ChemDraw
, 387
Chemical Abstracts
, 56
Chemical Abstracts Service, 384
Chemical complementarity, 38
Chemical Design Ltd., 387
Chemical genesis, 50, 56
Chemical Information Sources, Indiana University (CIS-IU), 380
Chemical intuition, 133
Chemical Society of Japan, 384
Chemical space, 4, 128, 160, 169, 172
Chemical stability rules, 35
Chemical structure, 171
CHEMICALC
, 266, 301
Cheminnovation Software, 387
Chemistry 4D-Draw
, 387
ChemNovel
, 68, 102
Chemometrics, 153, 154, 390
Chem-X
, 387
Cheng-Prusoff equation, 130
Chiral centers, 135
Chloramphenicol acetyltransferase (CAT), 31, 105
Chloramphenicol analogs, 196, 197, 293
Chlorothiazide, 293
Chlorpromazine, 293
Chromatography, 242, 295
Chymotrypsin, 47
Cimetidine, 293
Citrate, 47
Citrate synthetase, 105
CLASS
, 29
CLIP
, 302
CLIX
, 7, 16, 22, 45
CLOGP
, 147, 148, 164, 260, 263, 277, 293, 295, 299, 301
Clonidine analogs, 207
Cluster analysis, 94, 96, 97, 144, 226, 300
Cocrystallized complex, 74, 108, 112
Combinatorial chemistry, 93, 113, 299, 303
Combinatorial explosion, 15, 81
Combinatorial libraries, 97, 226, 299
Combining rules, 50
CoMFA coefficient contour maps, 209
CoMFA fields, 136, 147, 153, 154, 162, 173, 215
CoMFA lattice, 205
CoMFA limitations, 138
CoMFA models, 68, 105, 111, 208
CoMFA region description, 146
Comparative molecular field analysis (CoMFA), 21, 31, 44, 73, 87, 127, 134, 136, 137, 138, 150, 151, 164, 166, 191, 202, 205, 221, 282, 300
Comparative molecular moment analysis (CoMMA), 222
Comparative molecular similarity indices analysis (CoMSIA), 149, 150, 215
Compartments, 132
Compass
, 139, 216, 221, 226
Compensation effect, 138
Complementary error function, 344
Computational chemistry, 373, 396
Computational Chemistry List (CCL), 379, 385, 392
Computer-aided drug design (CADD), v, vi
Computer-aided ligand design (CALD), v, 2
Computer-aided molecular design (CAMD), v, 99, 113
Computer automated structure evaluation (CASE), 265
Computer-Chemie-Centrum, 384
Computer simulations, 323, 324
Computer viruses, 381
CONCEPTS
, 17, 49, 50
CONCERTS
, 17, 49, 51
CONCORD
, 31, 391
Conformation, 81, 83, 133, 141, 142, 186, 298
Conformational analysis, 4, 104, 207, 251, 296
Conformational bioactive, 47, 135, 142, 144, 186, 188, 195, 199, 302
Conformational databases, 44
Conformational effects, 277, 288, 296
Conformational energy of ligand, 95, 221
Conformational ensemble, 287
Conformational enthalpies, 39
Conformational searching, 13, 46, 47, 80, 93, 198
Conformational space, 49, 82, 98, 144
Congeners, 252
Connection points, 29
Connectivity, 243
Connolly surface, 46
Constitutive fragments, 255
Constraints, 50, 68, 86, 346
Continuum solvation model, 290
Corina
, 387
Correction factors, 258, 261
Corticosteroid binding globulin, 221
Coulombic potential, 145, 159, 187, 349, 300
Counterion condensation, 321, 322, 354
Counterions, 317, 319, 327, 329, 331, 347, 352
Covariance, 153, 190
Cricket Graph
, 387
Cross-correlation, 134
Cross-validated prediction error, 191
Cross-validated r-squared, 191
Cross-validation, 141, 151, 154, 156, 160, 169, 189, 190, 194, 202
Crossover, 219
Crystal field environments, 23
Crystallographic protein-ligand complexes, 47, 223, 225
Crystallographic soaking experiments, 6, 23
Crystallographic waters, 20, 46, 74
Crystallography, 1, 74, 82, 317, 320, 341, 396
Cubic box, 344
Curves, Dials and Windows
, 348
Cutoff distances, 332
Cyclic functional groups, 33
Cyclophilin, 289
Cyclopropane, 258
Cyclosporin A, 289
Cytochrome P450, 19, 166
Cytochrome P450cam substrates, 23, 224

D2 dopamine agonists, 205, 210
Daresbury Laboratory Chemical Database Service, 381
Darwinian laws, 192
Databases, 29, 56, 299
Daylight Chemical Information System, 387
DBMAKER
, 31, 56, 68
De novo design, 2, 18, 34, 35, 39, 44, 49, 67, 70, 89, 97, 111, 226
De novo design programs, 84, 93
Dead zones, 14, 34
Del Re charges, 36
DelPhi
, 47, 150
DeltaGraph
, 387
Descriptors, 87, 94, 96, 128, 132, 134, 135, 145, 149, 152, 163, 169, 171, 184, 189, 203, 208, 211, 215, 222, 241, 266
Design constraints, 70, 74
Design criteria, 112
Design methodologies, 68
Desolvation, 49, 52, 70, 133, 141, 150
Dexamethasone, 281
DGEOM
, 35
DHFR-MTX, 49
Diamond lattice method, 10, 25
Diastereoisomerism, 251
Diazepam, 293
Dielectric, 322, 356, 361, 364
Dielectric continuum, 353
Dielectric discontinuity, 353
Dielectric saturation model, 354
Diethyl ether, 268
Diffusion of ions, 323
Digital Equipment Corporation, 379
Dihydrofolate reductase (DHFR), 4, 19, 20, 23, 24, 27, 31, 35, 36, 39, 45, 47, 48, 50, 52, 105, 133
Dihydroxybenzoate, 105
Diltiazem, 293
Dipeptides, 288
Diphenhydramine, 293
Dipole-dipole interactions, 330
Dipole moment, 280, 282
Directed DOCK method, 45
Directed tweak algorithm, 82
Directory of Graduate Research
, 375
DISCO
, 143, 187
Disopyramide, 293
Disperse azo dyes, 164, 165, 170
Dispersion forces, 243, 246
Dissociation constant, 129
Distamycin, 105
Distance bounds, 82
Distance-dependent dielectric function, 322, 356
Distance geometry (DG), 15, 44, 46, 48, 104, 187, 202
Distance maps, 187
Distance matrices, 214
Distortion terms, 136
Distribution coefficients, 242, 269, 295
DNA, 46, 317, 318, 348, 352
A-DNA, 318, 320, 329, 355, 357
B-DNA, 318, 320, 322, 329, 339, 355, 356, 357, 364
D-DNA, 355
Z-DNA, 318, 320, 329, 357
DNA base pair geometry, 321
DNA bent, 327, 348
DNA bonding, 319
DNA capping, 361
DNA CGCGAATTCGCG dodecamer, 327, 328, 342, 349, 359, 361, 362
DNA droplet, 361
DNA groove hydration, 350
DNA groove narrowing, 320
DNA helical axis, 347, 348
DNA helicoidal descriptor, 321
DNA helix melting, 323
DNA helix parameters, 320, 360, 364
DNA hydrogen bonds, 319, 347, 357
DNA irregular, 327, 348
DNA major groove, 348, 353, 362
DNA minor groove, 348, 350, 356, 359, 362
DNA pitch height, 320
DNA propeller twist, 319, 360
DNA radial distribution, 341
DNA rise, 319
DNA spine of hydration, 350, 353, 359, 362
DNA triple helices, 355
DOCK
, 3, 15, 16, 27, 44, 68, 387
Docking, 15, 83, 90, 99, 113, 144, 148, 243, 283
L-Dopa, 289
D-optimal design, 139
Dose-response curves, 129
Drew-Dickerson dodecamer, 320, 327, 346, 350, 356, 360, 361, 364
Drug design, 103, 158, 171, 241, 295, 296
Drug discovery process, 57, 92
Drug molecules, v, 75
Drug-receptor interactions, 87, 129
Drug space, 18
Duplicate structures, 95
Dye fiber interaction, 164
DYLOMMS, 138
Dynamic ligand design (DLD), 17, 49, 51

Edges, 133
Effective pair potentials, 330
Efficacy, vi
Efficiency, 54
ELANA
, 9
Elastase, 45
Electronegative functionalities, 249
Electronic bulletin boards, 375, 392, 396
Electronic conjugations, 247
Electronic mail, 374
Electrostatic fields, 147, 150, 157, 159, 187, 208, 300
Electrostatic interactions, 2, 70, 244, 318, 327, 336, 353
Electrostatic potential fitted charges, 145
Electrostatics, 19, 88, 99, 110
Element libraries, 75
ELISA (Exhaustive Linker/Search Approach), 24, 35
Ellipsoid casting, 15, 44, 46
Encryption, 388
End points, 141
Endothiapepsin, 40, 101
Energy-based methods, 6
Ensemble of conformers, 287
Enthalpy, 169, 206
Entropic descriptors, 207
Entropic effects, 301
Entropy, 28, 136, 147, 169, 195, 224
Environmental toxicity studies, 299
Enzyme, 51
Enzyme induction, 141
Enzyme inhibitors, 2, 133
Equilibration, 335
Ergodic hypothesis, 325, 335
Essential fragments, 266
Euclidean distance, 214
Ewald summation, 333, 344, 346, 358, 363, 364
Excite
, 378
Experimental data, 112
Expert system, 44, 260
Explanatory power, 162, 169
Explicit counterion simulations, 360
Explicit solvent models, 356, 362, 363
Extended fragments, 266
Extrathermodynamic parameters, 244

Face-centered cubic (FCC) periodic boundary conditions, 332
Factorial analysis (FA), 151
Fast sphere-matching algorithm, 44
Fermi function, 284, 285
Fiber diffraction, 318, 320
Field-fitting, 145, 186, 187
File format compatibility, 103
File transfer protocol (ftp), 377, 392
Filters, 56, 84, 97
Fine Chemicals Directory
, 45
Fitness landscape, 128, 129, 192
FK506, 51
FK506 binding protein, 37, 40, 51, 108
FKBP-12, 23, 92, 105, 108
Flat landscape, 166
Flexibases, 46
Flexibility, 4, 9, 79, 83, 96, 135, 252, 288
Flexible compounds, 282, 286
Flexible fitting, 82, 216
FLOG
, 46
Flufenamic acid, 293
Fluid simulations, 291
Folate, 105
Folded conformers, 298
Force biasing, 335
Force field, 6, 88, 89, 100, 318, 330
Force-shifted function, 344
Forecasting, 189, 190, 227
FOUNDATION
, 31
Fractional factorial design, 139
Fragment connection methods, 2, 9, 24, 75
Fragment location methods, 2, 4, 18
Fragment placement methods, 4
Fragmental constant, 255, 256, 257, 261, 265, 272
Fragments, 39, 40, 41, 75, 261
Fraying, 347, 358
Free energy, 100, 130, 136, 207, 224, 253
Free energy perturbation (FEP), 100, 291
Fujiyama landscape, 166
Furan ring puckering, 321
Furosemide, 293

GABA-receptor antagonists, 289
Galaxy
, 378
GAMESS
, 388
Gaussian, Inc., 388
GEMINI
, 12, 36, 39
GenBank
, 381
Gene activator protein, 105
Generalized Born/surface area (GB/SA), 290
Genetic algorithms (GA), 16, 17, 33, 34, 44, 48, 49, 50, 76, 80, 86, 99, 185, 192, 218, 219, 221, 381, 396, 397
Genetic partial least squares (G/PLS), 139
Genetically evolved receptor models (GERM), 218, 226
Genetics Computer Group (GCG), 388, 396
GenStar
, 12, 36
Global minimum energy conformer, 142, 186
Global response surface, 128, 172
Glucose/galactose receptor, 101
Glucuronides, 298
Glycine, 259
Glycogen phosphorylase b, 223
GMSD format, 104
GOLPE
, 138, 147, 154, 165, 173, 191, 208, 224
Gopher
, 375, 377
Gordon Research Conferences, v, vi, 385
Grand canonical ensemble, 331, 355
Grand canonical Monte Carlo (GCMC), 355
Graphical-user interface (GUI), 102
GREEN
, 5, 18, 19, 20
GRID
, 5, 7, 18, 19, 20, 22, 31, 71, 72, 91, 103, 107, 138, 148, 154, 196, 205
Grids, 88, 136, 173
GROMACS
, 388
GROMOS
, 330, 331, 339, 357, 358, 359, 360, 388, 397
Groove hydration, 350
Groove narrowing, 320
GroupBuild
, 12, 22, 36, 40
GROW
, 12, 36, 39, 56, 71, 77, 80, 88, 106
GrowMol
, 12, 36, 38, 95, 96
Guanidine diphosphate, 44
Guanidine triphosphate, 44

Haloperidol, 293
Hammett equation, 166, 252, 253, 263
Hammett sigma parameter, 131
Hansch approach to QSAR, 131, 167, 184, 211, 253
Harvest
, 378
HASL
, 139, 151
Helix axis, 347, 348
Helix melting, 323
Helix parameters, 320, 321, 360, 364
Hemagglutinin, 22, 31, 45, 105
Hemiharmonic restraints, 347, 350
Hemoglobin, 19, 21
Hexagonal prism boundary conditions, 333
Hidden layers, 194
High blood pressure, 106
Hingerty sigmoidal function, 354
HINT
, 5, 18, 21, 138, 147, 162, 173, 207, 283, 300, 302, 388
HIPPO
, 44, 72
Hit list prioritization, 93
HIV-1 (human immunodeficiency virus) protease, 4, 19, 21, 27, 31, 37, 38, 40, 43, 48, 49, 51, 52, 84, 91, 96, 101, 105, 106, 108, 224
HIV-1 protease inhibitor, 105, 108, 131, 162, 188, 223
HIV-2, 91
Hodgkin similarity index, 213
Home page, ix, 377
HOMO, 149
Homology modeling, 1, 45, 56, 68, 106, 111, 196
HOOK
, 9, 22, 24, 29, 68, 76, 77, 86, 94, 102
Hot spots, 68, 71
Hotbot
, 378
HSITE
, 5, 18, 19, 20, 72, 103
Hückel molecular orbital theory, 270
Human carbonic anhydrase, 37, 40, 42, 197
Human Genome Project, 381
Hydrated surface area (HSA), 275
Hydration, 287
Hydrogen bond acceptor basicity, 245, 246
Hydrogen bond donor acidity, 245, 246
Hydrogen bonding fields, 300
Hydrogen bonds, 19, 23, 24, 31, 34, 36, 38, 40, 44, 51, 72, 77, 86, 89, 90, 143, 148, 184, 187, 225, 248, 252, 276, 356, 361
Hydrolysis, 166
Hydropathicity, 147
Hydrophilic folding, 248, 252, 288
Hydrophilicity, 282
Hydrophobic collapse, 248, 250, 288
Hydrophobic contacts, 51, 72, 107, 108
Hydrophobic descriptor, 202, 221
Hydrophobic effects, 38, 99, 147, 164, 195
Hydrophobic fields, 171, 207, 283, 300
Hydrophobic interactions, 21, 70, 244, 246, 250
Hydrophobicity, 19, 34, 40, 132, 138, 141, 150, 207, 246, 247, 276, 282
Hydroquinones, 45
p
-Hydroxybenzaldehyde, 276
p
-Hydroxybenzoate hydroxylase, 105
p
-Hydroxybenzoic acid, 259, 264
HyperChem
, 388, 397
Hypercube, Inc., 388
Hyperlinks, 377
Hypermolecule, 133, 200
Hypernetted chain (HNC) formalism, 323
HyperText Markup Language (HTML), 376
Hypertext transfer protocol (http), 377
Hypothetical active site lattice (HASL), 211

Idea generators, 4, 29, 36
ILIAD
, 10
ILIAD database
, 29
Imipramine, 293
Imperial College, 383
Implicit solvent models, 356, 362, 363
Incomplete sampling, 100
Indeno[1,2-c]pyridazines, 300
Indicator-type variables, 71
Indirect design, 73
Indomethacin, 105
Induced fit, 74, 79, 82, 83
Inductive logic, 140
Infoseek Ultra
, 378, 379
Inhibition constant, 54, 56, 130
Inhibitors, 2, 100, 223
Inktomi
, 378
ISIS
, 389, 397
ISIS/Draw
, 389
Institute of Scientific Information (ISI), 385
Interaction energy, 71, 88, 223, 243
Interaction sites, 23, 72
Interactive Simulations, Inc., 388
Intercorrelated descriptors, 209
Interface, 91, 101
Internal energy, 136
International Journal of Quantum Chemistry
, 394
International Union of Crystallographers, 385
Internet, 373
Internet Explorer
, 376, 389
InterNIC, 381
Intramolecular interactions, 247, 250, 295, 296
Inverse Boltzmann device, 91
Ion atmosphere, 318, 319, 322, 357
Ion-induced dipole interactions, 243
Ion pairing, 322
Ion-water pair correlation function, 351
Ionic bonds, 247, 248, 252
Ionic strength, 318, 322, 323, 353, 354
Ionization, 251
Irregular lattice, 27
Isoquinolines, 300
Isothermal-isobaric ensemble, 331, 332
Isotropic B factors, 364
Isotropic surface area (ISA), 275

JAVA, 377, 381
Journal of Computational Chemistry
, 394
Journal of Computer-Aided Molecular Design
, v, 393
Journal of Molecular Modeling
, 393

Karhunen-Loewe expansion (KLE), 151
KEY
, 21
Kinemage
, 388
Kinetic aspects, 130
Kinetic bottlenecks, 142
KLOGP
, 265, 295, 301
Klopman's method, 265
Knowledge-based potential function, 71
Kohonen map, 220

Latent variables, 189
Lateral validation, 134, 166, 168
Lawrence Livermore National Laboratory, 382, 385
L-Dopa esters, 289
Lead compounds, vii, 67, 134
Lead generation, 111, 113
Lead structures, 34
Leadings matrix, 151
LEAPFROG
, 12, 36, 44, 68, 73, 102
Leave-one-out (LOO) cross-validation, 141, 155, 185, 190, 225
LEGEND
, 12, 36
Lennard-Jones potential, 52, 137, 146, 147, 300
Lidocaine, 293
Ligand conformational energy, 95, 221
Ligand design, v, 1, 2, 3, 4, 37, 38, 40, 50, 51, 55, 159
Ligand flexibility, 15, 44, 45, 80
Ligand points, 24
Ligand-receptor interactions, 4, 86, 99, 145, 186, 197, 222, 282, 300
Ligand surface interaction energy, 221
Ligands, 34, 39, 70, 185, 188, 195, 197, 213
Linear free energy relationship (LFER), 128
Linear regression models, 194
Linear response approximation, 101
Linked-fragment algorithm, 23
Linker generation methods, 25, 26
Linkers, 2, 9, 11, 25, 28, 29, 33, 76
Lipid-water partitioning, 241
Lipophilic groups, 77, 90
Lipophilic interactions, 23, 283
Lipophilicity, 21, 148, 241, 247, 254, 271, 276, 303
Lipophilicity fields, 243, 295
Loading matrix, 151, 152, 153, 190
Local polarity, 278
Localized water, 350
LOCK
, 21
Lock and key theory, 158
Log D, 242
Log P, 50, 132, 148, 207, 215, 242, 275, 282, 290
LOOK
, 389
Los Alamos National Laboratory, 385
LUDI
, 7, 19, 22, 23, 34, 68, 72, 76, 77, 81, 87, 102, 107, 108
LUMO, 149
Lycos
, 378
Lysozyme, 19, 47, 105

MACCS
, 389
MacImdad
, 389
MacLogP
, 301, 388
MacroModel
, 397
Magellan
, 378
Magic constant, 256, 257
Major groove of DNA, 348, 353, 362
Manning theory, 321, 322, 353, 364
Manual intervention, 54, 111
Mathematica
, 388
MATLAB
, 389
Maximally dissimilar conformations, 46
Maximum variance, 152
MCDNLG
, 17, 49, 52, 108
MCSS
, 5, 18, 31, 68, 102, 103
MCY waters, 357
MD Toolchest
, 348, 350
MDL Information Systems, 389
MDL programming language, 397
Mean absolute error of prediction (MAEP), 157
MEDLINE
, 382
Merck Molecular Force Field (MMFF), 223
Meta analysis, 134, 166, 168
Meta-index
, 378
Metabolic simulation, 92
Metabolic stability, 92, 97
Metalloenzyme, 38
Methane, 258
Methotrexate, 23, 24, 35, 39, 45, 47, 48, 105
N
-Methylacetamide (NMA), 21
Michaelis-Menten constant, 130
Microcanonical ensemble, 331, 332, 362
MicroSimulations
, 389
Microsoft Corporation, 389
Microstates, 363
MidasPlus
, 27
MINDO
, 270, 279
Minimal topological difference (MTD), 133, 164, 200, 202, 211, 226
Minimum image convention, 333
Minireceptor, 196
Minitab
, 389, 397
Minor grooves, 348, 350, 356, 359, 362
MM3, 391
Model, 154, 159, 163, 324
MOL2MOL
, 103
MOLCAD
, 302
Molecular Applications Group, 389
Molecular diversity, 75, 300
Molecular dynamics (MD), 4, 51, 74, 98, 224, 286, 291, 318, 324, 352, 355, 359
Molecular electrostatic potential (MEP), 86, 278, 284
Molecular field, 135, 187, 206, 215, 282
Molecular fragments, 34, 72, 76
Molecular Graphics and Modelling Society, 385
Molecular interactions, 70, 205
Molecular lipophilicity potential (MLP), 138, 283, 288, 298, 300
Molecular mechanics, 145, 198, 223, 290, 335
Molecular modeling, 183
Molecular orbitals, 147, 149
Molecular recognition, 243, 247
Molecular shape analysis (MSA), 134, 198, 215, 221, 226
Molecular similarity/dissimilarity, 97, 198, 212
Molecular Simulations Inc. (MSI), 389
Molecular surface pattern matching, 44, 46
Molecular surfaces, 216, 278, 280
Molecular volume, 50, 245, 269
Molecular weight, 50, 280
MOLGEN
, 389
MOLMAKER
, 68
MOMEC
, 389
Monoamines oxidases, 300
Monte Carlo methods, 18, 21, 47, 80, 286, 291, 324, 352, 354
Monte Carlo minimization (MCM), 21, 48
MOPAC Pro
, 387, 389
MORASS
, 389
MORATE
, 389
Morphine, 105, 289, 298
Morphological properties, 348, 364
Mosaic
, 376, 389
MOZYME
, 389
Multiatomic fragments, 260, 261
MULTICASE
, 301
Multiconformation databases, 44
Multiple copy simultaneous search (MCSS), 5, 18, 20, 31, 68, 72, 81, 83, 89, 94, 102, 103, 106
Multiple linear regression (MLR) analysis, 132, 189, 199, 256, 265, 266
Mutation, 219
MVT-101, 21, 48, 106

National Institute of Standards and Technology, 385
National Institutes of Health, 385
National Library of Medicine, 385
National Science Foundation, 385
Nebivolol, 259, 264
Netropsin, 46
Netscape Navigator
, 376, 389
Neural networks, 132, 139, 151, 185, 193, 216, 389, 397
Neutral charge group, 330, 334, 339, 340, 344
NEWLEAD
, 9, 24, 33, 94
Newton's equations of motion, 324
NIPALS algorithm, 151
p
-Nitrotoluene, 253
NMR spectroscopy, 1, 74, 317, 319, 323, 325, 347
Nonbonded interactions, 330, 333, 336, 352
Nonlinear relationships, 193, 225
Nonoverlap steric volume, 199
Nonpeptide inhibitors, 108
Nonpolar interactions, 246, 249
Nootropic agents, 289
North Carolina Supercomputing Center (NCSC), 380, 385
Northern Illinois University, 380
Novelty, 56
Nuclear Overhauser effect spectroscopy (NOESY), 321
Nucleic Acid Database (NDB)
, 320, 325, 341, 364, 382
Nucleosides, 296
Nucleotide, 326

O
, 390, 397
n
-Octanol, 287, 296
Octanol/water partitioning, 252
Ohio Supercomputer Center, 379, 385, 392
Open Test
, 378
OPLS, 330
Optimization, 113
Oral bioavailability, 128
Organic solvents, 277
Orientation map (OMAP), 143
Outliers, 152, 154
Outside-in building methods, 77
Ovality, 280
Overfitting, 154
Overlap volume, 134, 199
Ovomucoid inhibitor (OMTKY3), 47
Oxford Molecular Group, 390

p21 ras protein, 44, 105
Pair correlation functions, 325, 338, 350
Pairwise additivity assumption, 330
Pairwise interactions, 333
Papain, 46, 223
Partial least squares (PLS), 136, 151, 153, 154, 189, 199, 209, 215, 295
Particle mesh Ewald (PME), 345, 363, 364
Particle type, 51
Partition coefficients, 241, 242, 252, 253, 255, 263, 267, 281, 303
Patent searches, 383
Patentability, 56
Pattern recognition, 139, 151
PCMODEL
, 390, 391
Pepstatin, 43
Peptides, 39, 76, 106, 287
Peptidomimetic inhibitor, 29, 73
Periodic boundary conditions (PBC), 332, 344, 363, 364
Persistence Analysis
, 348
Pharmaceutical companies, v, 4
Pharmacology, 97
Pharmacophore, 1, 106, 111, 135, 142, 186, 198, 211, 289
Pharmacophore model, 11, 31, 33, 34, 44, 51, 56, 68, 73, 94, 143
Phenobarbital, 293
Phenol, 292
Phenylacetic acids, 168
Phenytoin, 293
Phosphate group geometry, 327
Phospholipase A2, 107, 224
Physicochemical properties, 96, 128, 132, 189, 203, 215, 241
Pindolol, 259, 264
Pitch height, 320
Pittsburgh Supercomputing Center, 385
pKa, 222
PLA2 inhibitors, 19, 23
Placement of ions, 327, 328
PM3
, 145, 279
Point-by-point alignment, 186
Poisson-Boltzmann, 47, 150, 322
Polar groups, 248, 252, 256, 261
Polarity, 244, 245, 246, 247, 268, 269
Polarizability, 282
Pollutants, 299
Polyelectrolytes, 321, 355
Polyhalogenated aromatic compounds, 221
Pomona MedChem database
, 49
Pomona QSAR database
, 132
Population analysis, 145
Porcine pancreatic elastase, 72
Positional isomerism, 250
Potency, vi, 205
Potential energy surface, 335
Predictive power, 139, 162, 169
Preferential sampling, 335
PRESS, 154, 155, 190
Price of books, ix
Primary structure generation, 41
Principal components analysis (PCA), 134, 151, 152, 220, 274
Probabilistic search techniques, 48
Probes, 19, 148, 149, 187, 206
Procainamide, 293
Production phase, 335
Progesterone, 151
Progestogen receptor binding, 34
Programs, 301, 373
Projection to latent structures (PLS), 153
PRO LIGAND
, 9, 24, 34, 70, 77, 81, 84, 86, 96, 103
PROLOGP
, 294, 302
PROMETHEUS
, 34
Propafenone, 293
Propranolol, 293
N
-Propyl-apomorphine, 210
Protein Data Bank (PDB)
, 19
Protein-DNA complexes, 317, 325
Protein folding, 283
Protein Science
, 388, 394
Proteins, 1, 20, 72
Proximity effects, 247, 249, 252, 257
Pseudoreceptor, 1, 56, 196, 197
Publishers and journals, 393

QSAR and Modelling Society, 385
QUANTA/CHARMm
, 397
Quantitative structure-activity relationships (QSAR), 87, 91, 92, 127, 131, 132, 157, 166, 167, 184, 211, 253, 295, 383
Quantum Chemistry Program Exchange (QCPE), 301, 379, 390
Quasi-ergodic condition, 336
Quotes (familiar ones about computational chemistry), 383

Radial diffusion of ions, 323
Radial distribution, 342, 360
Random connection methods, 2, 17, 49
Random tweak algorithm, 28
Ranking, 94, 96, 97, 98
RasMol
, 390
Reaction field, 333
Receptor, 3, 4, 5, 16, 31, 34, 39, 46, 68, 70, 71, 73, 79, 81, 82, 86, 112, 128, 133, 143, 157, 184, 188, 195, 198, 200, 213, 299
RECEPTOR
, 17, 49, 53, 82, 143
Receptor flexibility, 55, 82, 99
Receptor mapping, 195, 200
Receptor models, 56, 68, 105, 111
Receptor surface models (RSM), 221, 226
Receptors, rigid, 54, 83
Reciprocal space, 345
Recognition forces, 241, 243, 282
Reduced amide pseudodipeptide, 106
Reduced fit, 198
Reference shape, 198
Regioisomerism, 250
Region selection, 208
Regression analysis, 197, 199, 203, 270, 271, 285, 290
Rekker's fragmental method, 256, 293
Relevance of descriptor fields, 169
REMOTEDISC, 202, 204, 226
Renin, 105, 106
Restrained molecular dynamics, 321, 346
Retinol, 105
Reversible inhibitor, 130
Reviews in Computational Chemistry
, ix, 394
Rhizopuspepsin, 39, 105
Ribbons
, 390
Ribose, 105
Rigid body fitting, 16
Ring systems, 24, 31, 77, 261
Ring-bracing algorithm, 28
RNA, 363
Robustness, 169
Rotatable bonds, 143
Royal Society of Chemistry, 386
RS[3]
, 390
Rugged landscape, 166
Rule-based methods, 3, 6, 54

Saccharose, 300
Salicylic acid, 259, 264
Salt bridges, 225
SAMPLS algorithm, 190
San Diego Supercomputer Center, 386
Sandia National Laboratories, 386
SAS, 390, 398
Scaffolds, 2, 9, 11, 28, 92, 128, 135
Scalar constraints, 74
SCARECROW
, 390
Science Citation Index
, 385
Score matrix, 151, 190
Scoring, 3, 11, 23, 29, 36, 38, 40, 42, 45, 47, 53, 55, 71, 75, 80, 83, 84, 85, 87, 88, 89, 90, 91, 95, 98, 100, 112, 113, 145, 224, 225
Screens, 97
Scripting tools, 104
SEAL
, 145, 150, 215
Seeds, 40, 50, 53, 77, 81, 92, 106, 112
Selection criteria, 112
Selectivity, 128
Self-coiling, 252
Self-consistency, 202
Semiempirical calculations, 145, 198
Sequential buildup methods, 2, 7, 12, 13, 36, 77, 78
Serena Software, 391
Series design methods, 185
Serotonin receptor ligands, 299, 300
SHAKE
algorithm, 347, 358
Shake-flask method, 242
Shape, 2, 70, 134, 213
Shifting functions, 333, 343, 358
Sialic acid, 22, 31
Sialidase, 224
Side chains, 39, 82, 83, 99
Side effects, 128
Sigmoidal dielectric function, 361, 364
Signal transduction pathways, 108
Similarity, 95, 149, 213
Simple cubic periodic boundary conditions, 332
Simplicity, 170
Simulated annealing methods, 21, 35, 44, 47, 52, 80, 81, 99, 144
Simulation engine, 324
Single-atom spacer, 33
Single atomic fragment, 260
Single-value decomposition (SVD), 151
Site point connection methods, 2, 6, 22
Site points, 6, 7, 8, 19, 23
SIV enzyme, 91
Skeleton, 29, 35, 42, 76, 77, 94
SMILES, 31, 267
SMILOGP
, 301
SMx, 290
SoftShell International, 391
Software, 373
Solvation, 6, 55, 71, 72, 81, 88, 89, 90, 99, 100, 221, 290, 300
Solvation free energies, 39, 286, 287
Solvatochromic parameters, 244<, 276br> Solvatons, 356, 358
Solvent accessible surface area (SASA), 88, 90, 148, 274, 284
Solvent-dependent conformational analysis procedure (SCAP), 287
Solvent-separated ions, 327, 350
Spacers, 24, 29, 33, 94
Spartan
, 391
SPASMS, 398
SPC waters, 350, 354, 357, 359, 363
Speed of the method, 101
Sphere coloring, 15
Spherical cutoff, 333, 363
Spine of hydration, 350, 353, 359, 362
SPLICE
, 9, 24, 31
Spreadsheet functions, 94
SPROUT
, 12, 36, 40, 56, 77, 94, 102
Squared deviation, 155
Stacking interaction, 247
Standard deviation of error of prediction (SDEP), 156
Standard error of prediction (SEP), 156
Statistical analysis, 154, 183
Statistically derived potentials, 91
Stepwise filtering, 95, 96
Stereoisomerism, 250
Steric complementarity, 213
Steric effects, 249
Steric field, 147, 157, 158, 300
Steric misfit, 133, 199, 200
Steric shielding, 249
Steroids, 34, 105, 151, 160, 168
Stochastic dynamics, 47
Strain energy, 50, 88, 97
Streptomyces griseus proteinase, 47
Structural parameters, 271
Structure-activity relationships, 34, 243
Structure-affinity relationships, 300
Structure-based drug design (SBDD), vii, 1, 67, 74, 111
Structure evaluation, 68
Structure generation, 68
Structures, 185
Subgraph addition, 24
Subgraph isomorphism algorithm, 82
Substituent constants, 184, 242, 253, 254
Substructure searching, 96
Substructures, 265
Superposition, 144, 203
Surface area, 50
Surface properties, 73
Surface tension, 277
Sweeteners, 105, 300
Switching functions, 333, 338, 344, 352, 360, 363
SYBYL
, 127, 143, 145, 157, 172, 208, 302, 391, 398
Sybyl Programming Language (SPL), 44, 104, 383
Synopsys Scientific, 391
Synthetic feasibility, 15, 44, 55, 76, 78, 86, 92, 93, 94, 97, 112, 113, 171
Systematic conformational search, 143, 187

TABLE
, 94
Taft steric parameter Es, 131
Target property, 135
Target sites, 35, 71, 72, 86, 112
Tautomerism, 250
TCP/IP, 374
Telnet, 377
Temperature, 336
Template joining operations, 94
Template library, 77
Tensor analysis, 215, 226
Test set, 144, 155, 194
Testing strategies, 56
Tetracaine, 293
Thermodynamic cycles, 100, 291
Thermodynamic integration, 100
Thermolysin, 38, 40, 88, 93, 95, 105, 188
Three-center hydrogen bonds, 361
Three-dimensional database searching, 9, 11, 15, 36, 46, 68, 82, 83, 93, 97, 226
Three-dimensional descriptors, 87, 94, 135
Three-dimensional QSAR, 21, 127, 153, 155, 183, 184, 195, 243, 282, 295, 300
Three-dimensional similarity measures, 94
Thrombin, 82, 95, 99, 105
Thymidylate-phenolphthalein, 49
Thymidylate synthetase, 19, 52, 105
Thyroid hormone analogs, 223
Time scale, 335
Tinker
, 391
TIP3P water, 356, 361, 362, 363, 364
TIP4P water, 353
TOPKAT
, 390
Topological distance, 257
Topological network, 133
Toxicity, vi, 92, 113, 128, 171, 221
Toxicology, 97
Traditional QSAR, 131, 167, 184, 211, 253
Training set, 140, 146, 153, 155, 158, 185, 194
Trajectory, 324, 325, 343
Transport properties, 97
TRIAD
, 10
TRIAD database,
11, 29
Trimethoprim, 293
Triosephosphate isomerase, 23, 105
Triple helices, 355
Tripos, Inc., 391
Trophozoite cysteine protease, 45
Truncation, 208, 333, 336, 338
Trypsin, 19, 20, 23, 24, 43, 99, 105
TSAR
, 302
Twin-range cutoff, 333, 357, 358, 364
Two-dimensional QSAR, 184
Two-dimensional substructures, 96
Two-phase pH-metric method, 242

UniChem
, 390, 391
Union surface, 218
Uniqueness of QSAR model, 170
United States Department of Defense, 374
UNITY-3D
, 143, 391
Universal Resource Location (URL), 376, 378
University of Minnesota Supercomputer Institute, 386
User-defined fragments, 266

Validation, 194, 348
VAMP
, 390
van der Waals contacts, 29, 38
van der Waals interactions, 70, 88, 94, 146
van der Waals intersection envelope volumes, 137
Variable scaling, 209
Variable selection, 165, 208
Variance, 132, 149, 189
Verapamil, 293
Verloop parameters, 134
Vertices, 133, 200
Virtual log P, 289, 298
Virtual Reality Modeling Language (VRML), 379, 383

Waste management, 171
Water, 249, 327, 328, 350, 352
Water-dragging technique, 276
Water-separated ion pair, 359
Watson-Crick hydrogen bonds, 319, 347, 357
Wavefunction, Inc., 391
WebCrawler
, 378
Webs, 46
WHAT IF
, 391
Whole molecule methods, 2, 15, 44
WIZARD
, 46
World Association of Theoretically Oriented Chemists, 398
World Wide Web, ix, 373, 375, 378

Xanthines, 296
XMOL
, 391
X-PLOR
, 391, 398
X-ray crystallographic data, 142, 144, 188
Xylene, 253

Yahoo
, 378, 379
YAK
, 195, 196, 221

Zidovudine (AZT), 171

Return to the RCC Table of Contents
Return to the RCC Indexes
Return to "Reviews in Computational Chemistry" home page

Copyright 2006-2009. All rights reserved.
Updated March 2009.
Webmaster: Donald B. Boyd, Ph.D., Indiana University-Purdue University at Indianapolis (IUPUI)