REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 16 (2000)

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.)

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Ab initio calculations, 141, 143, 162, 166, 232
Absolute binding free energies, 238, 247, 277
Absolute hydration free energies, 225, 234, 235
Absorption, distribution, metabolism, and excretion (ADME), 34
Acetaldehyde, 235
Acetamide, 233
Acetone, 235, 237
Acetonitrile, 245, 248
Acetylcholine, 56
Acetyltryptophanamide, 252
Acidity, 190
Acquired immune deficiency syndrome (AIDS), 254
Acquisition, 26
Activations, 124
Active sites, 190, 250
Activities, 124
Activity level, 124
Activity, 36
Adaline networks, 63, 83, 86
Adaptation, 75
Adaptive K-means algorithm, 99
Adaptive resonance theory (ART) networks, 64, 86, 88
Adenosine deaminase, 235, 257, 258
Adenosine monophosphate, 263
Adsorption at surfaces, 197
Adsorption isotherms, 193
Adsorption in zeolites, 191
Affinity constants, 36
Alanine, 236
Alditols, 91
Alkali cations, 243, 248
Alkali halides, 147
Alkali ion adsorption, 197
Alkali silicate glasses, 198
Alkanes, 236
All-atom force field, 227, 232, 255, 279
Allosteric binding site ligands, 263
AlO4, 166
ALOGP method, 233
Alpha-cristobalite, 182, 187
Alpha-lytic protease (ALP), 253
Alpha-quartz, 181, 185, 187, 188, 189
Aluminosilicate glass, 199
Aluminum phosphates, 186
AM1 calculations, 238, 278
AMBER
, 227, 228, 230, 232, 233, 234, 236, 237, 238, 244, 246, 247, 249, 250, 252, 253, 254, 255, 256, 261, 265, 267, 269, 271, 283
AMBER force field, 221, 243, 245, 246, 257, 260
Aminobenzamidine, 252
Aminopyrazolopyrimidine, 230, 231
Ammonia, 237
Amorphous materials, 173, 195
Amprenavir, 257
Analysis of neural networks, 120
Analytical chemistry, 96, 98
Anemia, 269
Angiotensin-converting enzyme (ACE), 32, 249
Anisole, 237
Annealing, 197
Anthracene, 238
Anti-Hebb learning, 82
Antibiotics, 245
Antibody, 267, 270
Antigens, 270
Antitumor drugs, 259
Aporepressor, 266
Aqueous solubilities, 93
Arabinose binding protein, 7
Argon, 192, 193
ARGOS
, 257
Aroclor, 97
Aromatic compounds, 236
Artificial intelligence (AI), 73, 74
Artificial neural networks (ANN), 53, 57, 88
Artificial neural networks software, 127, 128
Ascomycin, 269
Aspartic acids, 280
Associations, 71
Asynchronous mode, 63
Atom types, 161
Atomic charges, 236, 249
Atomic connectivity, 143
Atomic ionization potentials, 93
Atomic polarizability volumes, 148
Atomic polarization, 152
Atomic solvation potential, 6
Atomistic simulations, 177
Augmented consistent valence force field (cvff.aug), 185
Autoassociative networks, 62, 72, 86, 97, 108, 110
Autocorrelation vectors, 11
Available Chemicals Directory (ACD)
, 27, 28
Axon, 56
Azapurine, 235

Background correction, 70
Backpropagation networks, 66, 72, 75, 86, 88, 89, 90, 100, 110, 112, 121
Bacteriophages, 266, 271
Badger's rules, 174
Basis set 3-21G*, 279
Basis set 4-31G, 249
Basis set 6-31G, 232
Basis set 6-31G*, 227, 228, 230, 279
Basis set 6-31G**, 227, 228, 232, 235
Bayesian regularized backpropagation networks, 108
BCUT descriptors, 10
Beer's law, 71
Benz[cd]indole, 230
Benzamidine, 251, 252
Benzene, 234, 237, 238
Benzonitrile, 237
Bias, 121
Biased library design, 32
Bidirectional associative memory (BAM) network, 79, 83, 86, 88, 93, 125
Binary key, 8
Binding affinities, 218, 277, 283
Binding affinity prediction algorithm, 37
Binding conformation, 239
Binding site, 5, 14, 275
Bioactive compound, 218
Bioavailability, 232
Biological properties, 232
Biological targets, 4, 240, 249
Biosynthesis of aromatic amino acids, 266
Bit strings, 8
Blood glucose, 100
Blood-brain barrier penetration, 35
BLOGP method, 233
Boiling points, 100
Boltzmann machine ANN, 64, 86
Bond connectivity, 143
Bond dissociation energies, 93
Bond length constraints, 222
Bond stretching, 160, 164
Bond-PMF correction, 237
Boolean operations, 8
Born-Mayer-Huggins (BMH) ion potential, 196, 199, 200
Born-Oppenheimer approximation, 142, 154
Borosilicate glass, 199
BOSS
, 229, 233, 236, 257
Boundaries, 223
Boundary contour system networks, 87
Boxing algorithm, 26
Braced ligand, 6
Brain, 56
Brain-state-in-a-box (BSB) ANN, 64, 78, 86
Brain-state-in-a-box Hebb, 82
Branching properties, 10
Bridging hydroxyl groups, 190
Bridging oxygen, 198
BrØnsted acid sites, 190
Brownian entropy, 6
Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm, 93
BSB Widrow-Hoff rule, 83
Buckingham potential, 196
Bulk solvation effects, 252
Butane, 193

Calibration, 70
Calixarene, 247
Calixspherand, 247
Cambridge Structural Database (CSD)
, 28
Camphor, 260
Cancer therapy, 259, 261, 264
Capillary zone electrophoresis, 92
Carbohydrates, 271
Carbon tetrachloride, 233, 237
Carbonic anhydrase II, 258
Carbonyl compounds, 234
Carrageenans, 91
Cascade correlation networks, 91
Cascaded clustering, 21
Catalysis, 175, 177, 187, 190, 195, 196
Catalytic antibody, 267
Categorical data, 68, 103, 105
Category membership, 66, 117
Cathepsin D, 14, 33
Cation desolvation, 245
Cation mobility, 195
Cation-anion pair, 153
Cation-exchanged zeolites, 194
Cauchy machines, 86
CAVEAT
, 13
CEDAR force field, 221, 256, 257
Cell multipole methods, 158
Cell surface oligosaccharides, 271
Cellular uptake, 232
Centroid, 121
Ceramic modeling, 178
Ceramics, 175, 176, 177, 195
Charge equilibrium scheme, 175
Charge models, 150
Charge neutrality, 162
Charge polarization, 227
Charge-compensating cations, 195
Charged molecules, 232
Charges, 162, 275
CHARMM
, 261, 267, 269, 270
CHARMM force field, 221, 236, 252, 266, 270, 271
CHELP procedure, 238, 279
ChemDiverse
, 11, 30, 31
Chemical Abstracts Service database (CAST-3-D)
, 27
Chemical Design Ltd., 14
Chemical diversity, 3
Chemical industry, 141
Chemical shifts, 91, 116, 190
Chemical structure databases, 13
Chemometrics, 53
Cherry-picking procedure, 24, 30
Chi-squared test, 116
Chiral chromatographic separations, 92
Chiral substrates, 246
Chloride ion, 236
Chlorobenzamidine, 252
Chloroform, 233, 244, 246
Chlorophenol, 245
Cholecystokinin (CCK) antagonists, 32
Chymotrypsin, 252, 253
City block distance summation function, 77, 80
Class IV charges, 238
Classification, 64, 66, 70, 88
Classification problems, 86, 97, 99, 106, 114
ClogP
, 9, 22, 34, 233
Cluster analysis, 67
Cluster significance tests, 25
Cluster-based selection, 19
Clustering, 21, 25, 86, 97
Clustering methods, 70, 96
Clusters, 109
Coatings, 158, 175
Coesite, 182, 185
Coformycin, 257
Collections of processing elements, 85
CombiBUILD
, 14
CombiDOCK
, 14
Combinatorial chemistry, 1, 2, 53, 276
Combinatorial libraries, 3
Combinatorial library design, 1, 29
Combining rules, 173
Commercial compound directories, 3
Comparative molecular field analysis (CoMFA), 12
Compass
, 12
Competition, 74, 75
Competitive direct output, 79
Complementarity, 5
Compound libraries, 26, 28, 38, 53
Comprehensive Medicinal Chemistry database (CMC)
, 27
Compressibility data, 146
Compressing transformation, 103
Computational chemistry, 142
Computer simulations, 217
Computer-aided combinatorial library design, 1
Computer-aided molecular design, 2
CONCORD
, 8, 11
Configurational-bias Monte Carlo, 193, 201
Configurational space, 245
Conformational analysis, 277
Conformational energies, 175
Conformational entropy, 6
Conformational flexibility, 6, 13, 15, 31, 233
Conformations, 142, 144, 162, 217, 246
Connection table, 8
Connectionist hyperprism network, 100
Connections, 85
Connectivity, 160
Consistent force field (CFF), 156, 166, 192
CONSOLV
, 7
Constant pressure molecular dynamics, 189
Constant volume molecular dynamics, 196
Constrained dynamics, 222
Constrained library design, 32
Constraint profile, 8
Continuous numerical data, 105
Continuous property modeling, 95
Continuum models, 223
Convergence of free energy, 224, 283
Coordinate coupling, 232, 236
Coordination, 160
Core, 2, 152
Corepressor, 266
CORINA
, 8
Corporate chemical structure databases, 3, 15, 21, 22, 26
Correlation effects, 163, 228
Correlation coefficient, 119
Correlative component analysis (CCA), 106
Correspondingly connected layers, 85
Corrosion, 158, 175, 176, 177
Corrupted data, 73, 74, 97, 108, 125
Cost function, 117
Coulombic interactions, 142, 144, 158, 221
Counterpropagation ANN, 64, 87, 88, 94, 97, 109
COUSIN
, 23
Covalent hydration, 234, 258
Coverage design, 24
CPU time, 221, 285
Crack propagation, 199
Cro proteins, 266
Cross-validated correlation coefficient, 119
Cross-validation, 111
Crown ethers, 93, 239
Cryptands, 244
Crystal structures, 6, 13, 146, 163, 217, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 261, 262, 263, 265, 266, 267, 268, 269, 270, 271, 275, 276, 278, 279, 286
Crystal surfaces, 177
Crystalline solid, 145
Crystalline-to-amorphous transition, 189
Crystallite morphology, 177
Crystallographic B-factors, 276
Crystallographic shear planes, 176
Crystals, 145
Cumulative delta rule, 84, 89, 100
Cumulative sum, 76
Cut-off criteria, 221, 287
Cyanomethane, 232
Cyclic polyethers, 239
Cyclodextrins, 100, 245
Cysteine, 236
Cytochrome P450cam, 260
Cytosine, 227
Cytosolic protein, 269

D-optimal design techniques, 10, 24
Data analysis methods, 103
Data compression, 72, 73, 86, 100, 108, 118
Data fitting process, 170
Data preprocessing 102
Data reduction, 73
Data set dimensionality, 72
Data with discontinuities, 103
Database diversity, 28
Database search methods, 276
Daylight Chemical Information Systems software, 9
Daylight fingerprints, 17, 32
De novo drug design, 13, 33, 38, 276
Dealuminated zeolite, 181
Deamination of adenosine, 257
Deazapterins, 262
Decision boundaries, 99
Decisions, 120
Deconvolution, 70
Defects, 176, 177
Degree of connectivity, 85
Dehydroxystatine, 250
Delocalized electrons, 142
Delta bar delta (DBD) algorithm, 90
Delta rule, 83, 89
Denaturation, 267
Dendrites, 56
Dense silica polymorphs, 185, 195
Densities, 170, 200
Density functional methods, 163, 191
Deoxycoformycin, 257
Deoxyhemoglobin, 270
Dependent variables, 60
Descriptor space, 15, 24, 25
Descriptor validation, 8, 16, 36
Descriptors, 3, 4, 7, 8, 10, 11, 12, 13, 15, 18, 25, 30, 31, 35, 37, 38
Design in Receptor
, 14
Desolvation, 218, 250, 251, 273, 277
Desolvation free energy, 243, 285
Diabetes, 263
Dibenzo crown ethers, 243
Dielectric constant, 170, 221, 224
Dielectric continuum, 176
Dielectric properties, 170
Diffraction measurements, 195
Diffusion, 176, 179
Diffusion coefficients, 191, 193, 224
Diffusive regimes, 193
Digital filtering, 70
Dihydrofolate reductase, 259, 260
Dimension reduction, 86, 118
Dimethoxybenzene, 237
Dimethylamine, 237
Dimethylhistamine, 229
Dimethylpterin, 262
Dipole moments, 143, 152
Dipole-dipole interactions, 233
Directionality of chemical bonding, 148, 158
DISCOVER force field, 221
Discriminant analysis, 54, 66, 68, 69
Discrimination index, 118
Disilicic acid, 166, 168
Disordered glassy phase, 196
Dispersion interaction energy, 148, 163
Dissimilarity, 4, 12, 22
Dissimilarity-based compound selection, 20, 23
Dissolution processes, 176
Distamycin, 272
Distance-based measures, 25
Distributed memory, 74
Diverse property-derived (DPD) method, 22
DiverseSolutions
, 38
Diversity, 3, 24, 25, 28, 30
Diversity analysis, 1, 20, 35, 39
Diversity function, 13
Diversity space, 3, 7, 35
Diversity voids, 26, 31
DIVPIK
, 28
DNA, 259, 260, 266
DNA binding proteins, 265
DNA mutations, 272
DNA sequences, 100
DNA structure, 272
DNA-drug interactions, 272
DNA-hydrolyzing enzyme, 267
Docking, 277
Doublewide sampling, 282
Drug candidates, 2
Drug design, 98, 233
Drug discovery, 2, 39, 141
Drug targets, 4, 240, 249
Drug-receptor binding, 4, 5, 272
Druglike properties, 36
Drugs, 4, 15, 217, 253
Dual-topology, 282, 287
Dummy atoms, 281
Dynamics of networks, 85
DYSTAL network, 100

EAInventor
, 38
Edge design, 24, 26
Edge effects, 223
Effective input, 75
Einstein diffusion, 193
Elastase, 253
Elastic constants, 143, 170, 189
Elastic strain, 176
Elastin, 253
Electric field dependent force field for water, 194
Electrical conductivity, 199
Electrolytes, 175
Electron correlation, 235
Electron density, 152
Electron diffraction, 177
Electron microscopy, 176
Electron transfer, 150
Electronic displays, 158
Electronic effects, 143
Electronic properties, 10
Electrons, 142
Electrostatic decoupling, 232, 236
Electrostatic effects, 144, 189
Electrostatic energy, 221, 236
Electrostatic potential fitted charges, 163, 227, 238
Electrostatic potential surfaces, 275
Electrostatic profile, 5
Electrotopical state index, 22
Emphysema, 253
Empirical force fields, 168, 187
Empirical potential energy functions, 236
Empirical scoring functions, 14, 37
Empirical shell model potential, 187
Encoding, 103
Endopeptidase, 249
Endothelin antagonists, 17, 18
Energy, 144
Energy dispersion X-ray spectra, 98
Energy minimization, 275
Energy of desolvation, 5
Ensemble average, 220
Ensemble of networks, 113
Enthalpic binding energy, 5
Entropy, 5, 13, 218, 286
Enzymes, 218, 238, 239, 250
ENZYMIX
, 270
EPEN force field, 154
Epochs, 61, 90, 97, 110, 117, 121
Equilibrium, 155, 177
Equilibrium geometry, 144, 146, 154
Error, 90, 103, 220, 283
Error function, 75, 80
ESFF force field, 221
Ethane, 155, 232, 236, 237
Ethanol, 233, 234
Euclidean distance, 77
Excitatory weight, 87
Excitatory effect, 123
Excited state, 237
Excretion, 232
Experimental design, 24
Expert systems, 74
Explicit solvent, 223, 224, 275, 287
Exponential transfer function, 79
Extended delta bar delta (EDBD) algorithm, 90
Extended X-ray absorption fine structure (EXAFS), 195, 198
Extrastatistical quality, 116
Ewald summation, 158, 177, 222

False alarm rate, 115
False negative (FN) decision, 115
False positive (FP) decision, 115
False positive ratio, 115
Fast learning, 90
Faujasite, 183, 187, 191
Feedback networks, 62
Feedforward networks, 62
Ferrierite, 193, 194
Fibrinogen receptor antagonists, 17
Final state, 220
Fingerprints, 8
FK506 binding protein, 268, 269
Flashcard algorithm, 91
Flexibility of molecules, 6, 10, 13, 15, 31, 233
Flexible binding pocket, 276
Flexible docking of ligands, 13
Flexible zeolite framework, 194
FlexX
, 7
Fluorescence spectra, 92, 98
Fluorobenzamidine, 251
Fluorocarbons, 237
FOCUS-2-D method, 32
Focused library design, 3, 15, 32
Folate, 260
Force constants, 143, 164
Force field parameters, 143, 160, 168, 189, 257, 275, 279, 280
Force field transferability, 170
Force fields from ab initio calculations, 161, 166
Force fields, 141, 144, 145, 154, 156, 201, 238
Formal charges, 162
Formaldehyde, 235, 237
Four-point pharmacophores, 12, 14
Fourier series, 142, 157
Fourier transform, 98
Fracture surfaces, 199
Framework, 194
Framework topology, 181
Free energy, 217, 219
Free energy calculations, 240, 286
Free energy of binding, 5
Free energy of denaturation, 267
Free energy of hydrophobic interactions, 6
Free energy minimization, 187
Free energy perturbation (FEP) calculations, vii, 37, 218, 225, 236, 244, 273
Freeware, 126
Fructose 1,6-bisphosphatase, 263
Fructose 6-phosphate, 263
Fully interconnected layers, 85
Functional groups, 13
Fuzzy clustering, 22
Fuzzy logic, 26, 74

G-DNA quadruplex, 272
Galactose, 271
GAMESS
, 228
Gas chromatographic retention indices, 92, 95
Gaussian
, 227, 228, 229, 232, 279
Gene activation, 269
General diverse library, 3
General library design, 15, 29, 32
General representative library, 3
Generalization, 111
Generalized Born/surface area (GB/SA), 224, 238, 246
Generalized regresssion networks (GRN), 90, 96
Genetic algorithms, 30, 101
Geometric diversity, 13
Geometry optimization, 164
Gibbs free energy, 220
Glass surface, 197
Glasses, 195
Glaucoma, 258
Global minimum, 90, 112, 125
Global network dynamics, 87
Global response quality, 114
Globular proteins, 64, 270
GLOGP method, 233
Gluconeogenesis, 263
Glucose, 245
Glycolysis, 268
Gradient descent method, 90
Grain boundaries, 177
Graphical inspection, 277
Grid-based energetics, 276
GROMOS
, 234, 245, 248, 251, 254
GROMOS force field, 221, 243, 250, 256
Grossberg outstar layer, 83, 87, 95, 97
Ground state, 237
GTP-binding protein, 264
Guanosine triphosphate (GTP), 264

Hamiltonian, 219, 238
Hammerhead docking algorithm, 12
Hamming network, 87
Harmonic spring, 152
Harmonic spring constant, 153
HARPick
, 29, 30, 32
Hartree-Fock method, 163
Hash code, 28
Hashed fingerprints, 10
Hashing, 9
Heat bath, 194
Heat capacities, 170
Heats of adsorption, 193
Heats of sublimation, 163
Hebb rule, 81
Hebbian learning, 82
Helmholtz free energy, 219
Hemoglobin, 269
Henry constants, 192
Heteroaromatic compounds, 234, 235
Heteroassociative networks, 62, 86, 93, 96
Heuristic search methods, 30
Hexane, 193
Hidden layer processing elements (PEs), 72, 121
Hidden layers, 59, 86, 91, 99
Hidden node pruning, 92
Hierarchical clustering, 22, 121
Hierarchical scene structure networks, 87
High performance liquid chromatography (HPLC), 92
High temperature superconductor, 178
High-dimensional data, 97
High-throughput screening, 20, 34, 276
Highly constrained simulations, 223
Histamine, 227, 229
Histogram equalization, 103
Hit rates, 16
HIV-1 protease, 6, 39, 254, 277, 279
HIV-1 protease inhibitors, 218, 273, 278
Holorepressor, 266
Hooke's law, 142
HookSpace
, 13
Hopfield networks, 73, 82, 86, 88, 94, 97, 110
Human carbonic anhydrase II (HCAII), 258
Human immunodeficiency virus (HIV), 254
Hybrid networks, 87
Hybrid potential function, 173
Hybridization, 160
Hydrated zeolites, 194
Hydration, 229, 236
Hydration free energies, 233
Hydrogen bonds, 5, 224, 230, 233, 237, 247, 249, 256, 275, 279, 284
Hydrophilic characteristics, 245, 275
Hydrophobes, 5
Hydrophobic characteristics, 245, 275
Hydrophobic interactions, 6, 260, 279, 284
Hydroxybenzoic acid, 245
Hydroxyethylamine, 254
Hydroxypyrazole, 228
Hydroxypyridine, 227
Hydroxypyrimidine, 227
Hyperbolic transfer function, 78
Hypothesis testing, 125
Hysteresis, 259

IcePick
methodology, 12
Image analysis, 70
Imidazoledistamycin, 272
Iminocytosine, 227
Immunosuppressant agents, 269
Implicit solvent models, 223
Inactivity, 36
Inclusion complexes, 245
Incremental free energy changes, 220, 238
Independent variables, 60, 69
Induced dipole cohesion, 148
Inductively coupled plasma-atomic emission spectra, 94, 96
Infection, 271
Information, 58
Infrared reflectance spectra, 91
Infrared (IR) spectroscopy, 88, 91, 98, 110, 116, 117, 143, 190
Inhibitors, 158, 218, 235, 239, 248, 254, 257, 258, 259, 263, 277, 278, 282, 285
Inhibitory weight, 87
Inhibitory effect, 123
Initial state, 220
Inorganic carbonates, 149
Inorganic materials, 142, 145, 169, 174, 176, 201, 202
Inorganic oxides, 169
Inosine, 257
Input layer, 59, 89
Input processing elements (PEs), 58, 62, 65
Interfaces, 202
Internal coordinates, 155, 164
Interstitial positions, 172, 176
Intramolecular hydrogen bonding, 230
Intraocular pressure, 258
Ion interaction chromatography, 92
Ion mobility spectometry, 92, 107
Ion pair force fields, 158
Ion pair potentials, 144, 145, 157, 159, 187, 196, 201
Ion radii, 244
Ion-scattering spectroscopy (ISS), 198, 199
Ion-selective properties, 248
Ionic crystals, 143, 144
Ionic forms, 225
Ionic materials, 201
Ionization, 232, 247
Ionization energies, 148
Ionophores, 243, 245
Iron oxide, 176
Iron-containing enzymes, 260
Isosteric heats of adsorption, 192, 193

K nearest neighbor (KNN), 98
K-d trees, 24
Ketose-aldose isomerism, 268
Kirkwood-Müller formula, 193
Kohonen layer, 87, 95, 97
Kohonen network, 68, 86, 100
Kohonen maps, 25
Kohonen rule, 83
Kohonen self-organizing map (KOM) networks, 88, 97, 108
Kovats indices, 95
Krypton, 192

Langevin dipole model, 222
Laplace transform, 98
Large data sets, 68, 72
Laser desorption-ion mobility spectometry, 92
Laser-induced fluorescence spectra, 92
Laterally connected networks, 97, 107
Lattice dynamics, 187
Lattice energy, 146, 147, 190
Lattice energy minimization, 181, 182, 183, 184, 186
Lattice parameters, 170
Lattice relaxation, 194
Lattices, 145, 176
Layers, 108
Lead compounds, 4, 15
Lead generation, 16, 20, 276
Lead optimization, 21
Lead-containing glasses, 200
Learned information, 61
Learning, 75, 94, 95, 111, 122, 123
Learning coefficients, 80
Learning difficulties, 95
Learning inputs, 62
Learning rates, 80, 90, 110, 123
Learning rules, 58, 60, 62, 63, 80, 83, 87, 125
Learning stability, 87
Learning vector quantizer (LVQ) network, 64
Lectins, 270
Lennard-Jones parameters, 173, 221
Lennard-Jones potential, 173, 192
Library design, 15, 29, 30, 37, 276
Library searching, 73
Ligand binding, 6, 217, 218, 223, 234
Ligand optimization, 274, 277, 286
Ligand-receptor complex, 5
Ligands, 4, 5, 218, 221, 276
Linear direct output, 79
Linear discriminant functions, 106
Linear scaling, 104
Linear transfer functions, 77, 92
Linearly separable data set, 69
Lipophilicity, 232
Local minimum, 90, 91, 112, 113, 125
Local ordering of water, 6
Local symmetry coordinates, 163
Log P, 232
Lone pairs, 142
Long-range forces, 221, 228
Lorentz-Bertholet mixing rules, 173
Low density lipoprotein, 22
Low energy electron diffraction (LEED), 177
LUDI
, 14
Lyases, 257
Lysine, 236
Lysozyme, 271

MACCS Drug Data Report database(MDDR)
, 27
MACCS keys, 9
MACPRO force field, 269
MacroModel
, 246
Macromolecular binding site, 225
Macromolecular simulations, 223
Macromolecular targets, 240
Macromolecule-ligand complexes, 239
Macromolecules, 238
Macroscopic properties, 192, 196
Madaline networks, 83, 86
Madelung constants, 145
Majority, 77
Mannose binding protein, 270, 271
Many-body polarizable potential, 237
Mapping, 71, 100, 118
Markush representations, 38
Masking field networks, 87
Mass spectra, 91, 92, 98
Massachusetts Institute of Technology Research Laboratory of Electronics, 63
Materials modeling, 141
Materials science, 175, 201
Materials simulation, 151
Matthews coefficient, 116
Matrix isolation IR spectra, 91
Maximal dissimilarity selection, 34
Maximal overall diversity, 24
Maximally diverse set, 21
Maximizing pharmacophore diversity, 31
Maximum dissimilarity-based selection, 21, 22
MaxMin dissimilarity measure, 23
Maxprop algorithm, 90
MaxSum dissimilarity measure, 23
Maybridge database
, 27
MCY water models, 224
Mean absolute error, 119
Mean squared error (PRESS), 119
Membranes, 245
Memorization, 95, 109
Metabolism, 232
Metal oxides, 175, 195
Metallic inclusions, 199
Metallic systems, 149, 173
Methane, 192, 193, 237
Methanethiol, 232
Methanol, 193, 233, 234, 236, 237, 243, 244, 248
Methotrexate, 259, 260, 261, 262
Methylamine, 237
Methylbenzamidine, 252
Methylimidazole, 227
Methylphenol, 245
Methylpterin, 262
Michaelis complexes, 268
Microelectronics, 196
Microporous materials, 173, 180
Middle layer, 59
Minimum, 77
Minimum dissimilarities, 13
Minimum weight spanning tree (MWST), 25
Missing force field paramenters, 279
Missing residues, 273
Mixed solvent, 244
Mixed-alkali effect, 198
Mixed-mode Monte Carlo/stochastic dynamics, 246
MM2 force field, 175, 221
MM3 force field, 175, 221
MM4 force field, 221
MMFF force field, 221
Model validation, 280
Modeling, 70
Modulation functions, 98
Molecular diversity, 3, 26
Molecular diversity analysis, 1, 29
Molecular dynamics, 143, 176, 180, 188
Molecular dynamics simulations, 151, 191, 192, 197, 281
Molecular fields, 4
Molecular mechanics, 144, 149, 154, 218
Molecular mechanics force fields, 157, 158, 159, 167, 184, 187, 195, 201, 218, 220
Molecular modeling, 141
Molecular recognition, 3
Molecular similarity, 3
Molecular shape, 35
Molecular surface, 11, 12
Molecular targets, 218
Moments, 98
Momentum, 90
MonsterGauss
, 230
Monte Carlo (MC) methods, 176, 193, 224
Monte Carlo simulations, 143, 151, 191, 232
Mordenite, 184, 187, 193
Morphology, 177
Morse function, 164
Møller-Plesset perturbation theory calculations, 227, 228, 230, 235
Mulliken charges, 238
Multibody potentials, 149
Multidimensional scaling (MDS), 10, 24, 73, 98
Multipharmacophore molecular descriptors, 31
Multiple binding modes, 7
Multiple-copy simultaneous search (MCSS), 252
Multivariate nonlinear calibration, 92
Murine myeloma protein, 270
Mutation, 220
Myoglobin, 269

Naphthalene, 238
National Cancer Institute database (NCI-3-D)
, 28
Natrolite, 194
Near-infrared spectroscopy, 100, 107
Near-optimal solutions, 125
Nebularine, 257
Neighborhood behavior, 16
Neocognition networks, 87
Nerve signals, 56
Network architecture, 85, 122, 125
Network set-up, 108
Network stability, 87
Network topology, 58
Neural network software, 126, 127, 28
Neural Networks
, 124, 125
Neural networks, 54, 58, 63
Neural networks: Adaline, 86
Neural networks: Adaptive resonance theory, 86
Neural networks: Autoassociative, 62, 72, 86, 97, 110
Neural networks: Backpropagation, 72, 86, 88, 89, 100, 110, 112, 121
Neural networks: Bayesian regularized backpropagation, 108
Neural networks: Bidirectional associative memory, 83, 86, 88, 93
Neural networks: Boundary contour system, 87
Neural networks: Brain-state-in-a-box, 64, 78, 86
Neural networks: Cascade correlation, 91
Neural networks: Connectionist hyperprism, 100
Neural networks: Counterpropagation, 64, 87, 88, 94, 97, 109
Neural networks: Feedback, 62
Neural networks: Feedforward, 62
Neural networks: Hamming, 87
Neural networks: Heteroassociative, 62, 86, 93, 96
Neural networks: Hierarchical scene structure, 87
Neural networks: Hopfield, 73, 82, 86, 88, 94, 97, 110
Neural networks: Hybrid, 87
Neural networks: Kohonen, 68, 86, 100
Neural networks: Madaline, 83, 86
Neural networks: Masking field, 87
Neural networks: Neocognition, 87
Neural networks: Perceptron, 86
Neural networks: Radial basis function, 90, 99, 123
Neural networks: Recirculation, 100
Neural networks: Rumelhart-Zipser, 87
Neural networks: Self-organizing map, 64, 68
Neural networks: Sparse distributed memory, 86
Neural networks: Wavelet, 100
Neuron, 56, 57
Neurotransmitter, 56
Neurotropic activity, 269
Neutral molecules, 232
Neutron scattering data, 196
NevProp4
, 127
Newtonian dynamics, 193
Newtonian equations, 188
Nicotinamide adenine dinucleotide phosphate, 260
NMR spectroscopy, 91, 116, 190
Noble gases, 192
Node, 57
Noisy data, 74, 107, 125
Non-atom-centered partial charges, 154
Nonactin, 247
Nonaqueous solvents, 245
Nonbonded energy, 221
Nonbonded interaction potentials, 151
Nonbonded interactions, 173, 201
Nonbridging oxygen, 198, 199
Nonclassification, 118
Noncombinatorial libraries, 37
Noncomplementarity, 5
Nonformal charge models, 150
Nonframework cations, 174
Nonhierarchical clustering algorithm, 21
Nonlinear data, 72, 96
Nonlinear multivariate data, 93
Nonlinear principal components, 125
Nonlinear problems, 63
Nonlinear regression technique, 90
Nonlinear statistical mapping, 73
Nonlinearly separable data set, 69
Nonnumerical data, 105
Nonphysical charge distribution, 150
Nonphysical transformation, 264, 281
Nonprotein-ligand complexes, 239
Nonstandard residues, 275
Nonstationary data, 96
Nonuniform binning, 10
Normalized cumulative delta rule, 84
Normalized output, 79
Nuclear magnetic resonance (NMR), 6, 91, 195
Nuclear scintillators, 200
Nuclear waste, 200
Nucleic acid bases, 238
Nucleic acids, 141
Nucleosides, 233

Observables, 162
Octanol, 9, 233, 234
One-layer network, 59
One-of-N codes, 105, 113
OPLS force field, 221, 232, 236, 238, 243, 252, 257, 269
Optic nerve damage, 258
Optical fibers, 196, 197
Optical sensor array data, 100
Optimal brain damage pruning, 125
Optimization, 70, 86
Optimization of lead compounds, 276
Oral absorption, 34
Organic compounds, 142
Organic force fields, 173, 174
Organic molecules, 142, 149, 154, 221, 245
Organic polymers, 169, 201
Organic sorbates, 158
Outliers, 103
Output function, 75, 79
Output layer, 59, 95
Output processing elements (PEs), 58, 62
Overfitting, 109, 125
Overtraining, 109, 111
Oxidases, 260
Oxidation state, 160
Oxidation state charge models, 150
Oxide materials, 169
Oxopyridine, 227
Oxopyrimidine, 227
Oxygen diffusion, 179

Pair potentials, 172, 200
Pairwise interactions, 145
Pairwise potential models, 150
Pancreatic trypsin inhibitor (PTI), 252
Parameter estimation, 70
Parameterization, 218
Parameters, 143, 189
Parke-Davis corporate database (CBI)
, 27
Partial atomic charges, 232, 252
Partial charge model, 150, 279, 281
Partial least squares (PLS), 92
Partially flexible zeolite framework, 194
Partition-based selection, 19
Partition coefficients, 9, 22, 34, 223, 233
Partition function, 218
Partitioning, 22, 25
Parzen estimation, 96
Pattern recognition, 54, 88
Pattern unit, 99
Pearson product-moment correlation coefficient, 119
Pentaglyme, 244
Pentane, 193
Pepstatin, 33, 250
Peptide bonds, 248
Peptides, 233
Peptidomimetic inhibitors, 277, 285, 286
Perceptron, 63, 78, 82
Perceptron learning rule, 125
Perceptron networks, 86, 98
Perceptron Simulator for Drug Design (PSDD)
, 128
Performance metrics (PMs), 113
Periodic boundary conditions, 177, 223, 279, 287
Periodic solids, 143
Periodic systems, 162
Peroxisome proliferator-activated receptors (PPARs), 32
Perturbation theory, 148
Perturbed state, 220
Pharmaceutical activity, 53
Pharmaceutical industry, v, 2, 11, 141
Pharmacophore descriptors, 15
Pharmacophore diversity, 11, 28
Pharmacophore keys, 11, 23
Pharmacophore space, 23
Pharmacophores, 14, 23, 31, 36
Phase changes, 187
Phase transitions, 160
Phenol, 234, 237
Phenol ionization, 247
Phenylalanine, 250
Phonons, 170
Phosphate mimics, 264
Phosphorylcholine analogs, 270
Photocatalytic degradation, 93
Photoelectron spectroscopy (PES), 198
Pictorial representation of free energy changes (PROFEC), 272
Piezoelectric crystal data, 92
Pigments, 175
pKa values, 232, 275
Plasmepsin II, 14
PM3/CM1p method, 238
Podand ionophore, 246
Point charges, 143, 221
Point defects, 145, 176
Point polarizable ion model, 152
Polar molecular surface area, 34
Polarizability, 148, 152, 153, 237
Polarizable water, 238
Polarization, 188, 195, 222, 232, 237, 244
Pollution control, 175
Polymer simulations, 158
Polymers, 201
Population analysis, 163
Porcine pancreatic elastase, 253
Positive predictive value, 115
Post-Hartree-Fock methods, 163
Potential energy surfaces, 93, 143, 155, 162, 168
Potential function based network, 101
Potential function parameters, 171, 232
Potential of mean force (PMF), 237, 247
Powder diffraction, 176
Precision, 115
Preorganized hydrogen bond donors, 247
Pressure-induced structural transitions, 189
Principal components analysis (PCA), 10, 24, 54, 69, 92, 96, 106
Privileged fragment, 32
PRO_LIGAND
, 13
PRO_SELECT
, 13, 33
Probabilistic neural networks (PNN), 91, 97
Processing element (PE), 57, 74
Processing element outputs, 124
Processing unit, 57
Product-based library design, 30
Product-based selection, 30, 37
Prokaryotic repressors, 266
PRONET
, 128
Propane, 193, 194, 236, 237
Propanol, 234
Property fingerprints, 11
Property prediction, 95
Property space, 26
Protease inhibitors, 248
Proteases, 249
Protein conformational entropy, 6
Protein crystallography, 6, 13, 217, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 261, 262, 263, 265, 266, 267, 268, 269, 270, 271, 275, 276, 278, 279, 286
Protein dynamics, 6
Protein folding, 93
Protein structure, 37, 217
Protein surface, 223
Protein translocation, 269
Protein-ligand complex, 4
Proteins, 3, 14, 17, 64, 141, 222, 270
Protonation states of amino acid residues, 275
Prototype layer, 99
Pruning methods, 106, 122
Pteridine, 235
Purine, 235
Purine riboside, 258
Pyrimidine, 235
Pyruvic acid, 235

QCISD(T) method, 235
Quantitative structure-activity relationships (QSAR), 10, 35, 38, 70, 89, 95, 128
Quantum chemically derived potentials, 187
Quantum Chemistry Program Exchange (QCPE), 128
Quantum mechanical calculations, 148, 150, 162
Quantum mechanical methods, 142
Quantum mechanics, 147
Quartic force constant, 165
Quickprop
, 90
Quinazoline, 235

Radial basis function networks, 90, 99, 123
Radial distribution functions, 196
Raman spectra, 92, 110
Rapamycin, 269
Ras protein, 264
Reaction field, 222, 234
Reaction rate equilibria, 223
Reactions, 98
Reactive potential, 143
Reagent-based selection, 29, 37, 38, 39
Recall, 115
Recall mode, 61
Receiver operating characteristic (ROC) curves, 120
Receptor binding, 232
Receptor site, 3
Receptor-based descriptors, 13
Receptor-relevant subspace, 10
Receptors, 5
Reciprocal nearest-neighbor algorithm, 22
Recirculation networks, 100
Reduced data set, 72
Reductases, 260
Redundancy, 26
Redundant compounds, 20
Redundant coordinates, 163, 164
Reference library, 31
Reference state, 220
Refractive index, 93
Regression analysis, 54
Reinforcement learning, 62
Relation factors, 123
Relative binding free energies, 218, 238, 254, 257
Relative catalysis free energies, 254
Relative hydration free energies, 257
Relaxation effects, 228
Reliability index, 116
Representative sampling, 16
Representative subsets, 25
Representative training, 107
Repressor, 266
Resolution, 70
Response quality for a category, 114
Retention indices, 93, 95
Retinoic acid ligand binding domains, 6
Reverse sampling, 36
RGD (Arg-Gly-Asp) loop, 17
Rhizopus pepsin, 250
Ribonucleases, 265
Ribosomal RNA, 265
Rigid lattices, 194
Rigidity, 193
Ring-cluster hash code, 28
RNA sequences, 100
RNase A, 265
Root-mean-square error (RMSE), 119
Rotational isomeric state (RIS), 201, 236
Rotational motion, 5
Round-robin-connected layers, 85
Rule learning, 122
Rule of five, 34
Rule-based force fields, 174, 192
Rules of learning, 58, 60, 62, 63, 80, 83, 87, 125
Rumelhart-Zipser networks, 87

Salt effects, 223
Sammon mapping, 25
Sampling, 16
Sampling of conformational space, 246
Sampling times, 244
Saturated processing elements (PEs), 112
Scaffold, 2, 29, 33, 37
Scaling, 65, 74, 103, 105, 112
Scaling charges, 234
Scanning electron microscopy images, 98, 177
Schrödinger equation, 142, 144
Scientific Computing and Automation
, 102
Scoring function, 12, 30
Screening, 4, 8, 9, 20
Secondary protein structure, 91, 93, 116
SELECT
, 32
Selection of reagents, 29
Self-diffusivities, 193
Self-organizing map ANN, 64, 68
Sensitivity, 115
Sensitivity analysis, 122, 123
Serine protease, 252, 253
Serum lectins, 270
SHAKE method, 222, 279
Shape properties, 10, 31
Shareware, 126
Shear structures, 176
Shell model potentials, 145, 152, 187, 201
Short-range repulsive energies, 148
Sickle cell mutant, 270
Sigmoid transfer function, 78
Sign transfer function, 78
Signal processing, 70
Signaling pathways, 264, 269
Signaling proteins, 264
Significance testing, 122
Silicalite, 181, 184, 187, 193
Silicates, 150, 169
Silicon oxide, 166
Similarity, 3, 12
Simplex method, 110
Simulated annealing, 24, 30
Simulated data, 108
Simulation of liquids, 149
Sine transfer function, 78
Single topology method, 281, 283, 288
Singletons, 21
SiO4, 166
Site-directed library design, 14, 15
Site-directed ligand design, 4
Slow growth (SG), 218
Slow learners, 90
Small organic molecules, 238
Smoothing, 70
Sodalite, 183, 189
Soft independent modeling by class analogy (SIMCA), 96
Soft output, 79
Softmax, 79
Software, 54, 126
Solid phase synthesis, 1
Solubility, 223
Solute-solvent interaction, 236
Solvation, 223, 236
Solution conformation, 244
Solvation free energies (SFEs), 221, 233
Solvent entropy, 6
Solvent molecules, 223, 224, 279
Solvent-accessible surface, 275
Solvophobic interactions, 36
Soma, 56
Sonar signals, 121
Sorbates, 189, 194
Spanning trees, 25
Sparse data, 96
Sparse distributed memory networks, 86
Spatial cross talk, 90
SPC water models, 224, 238
SPC/E water models, 224, 275, 279, 287
Specific atom layer descriptors, 10
Specificity, 5, 115
SPECS database
, 27
Spectral library, 72
Spectroscopic force constants, 155
Splined potentials, 151
Splines, 93
Spread design, 24
Spresi database
, 16, 36
ST2 water models, 224
Stability, 87
Standard Drugs File
, 31, 32
Standard score, 104
Staphylococcal nuclease, 267
State variable, 220
Static dielectric constants, 170
Statine, 250
Stationary point, 143
Statistical methods, 54, 68
Statistical thermodynamics, 219
Statistics, 66, 73
Step function, 79
Stereochemical preference, 256
Stereospecificity, 250
Steric bulk, 13
Steric energy, 142
Steroid biosyntheses, 260
Stishovite, 182, 185
Stochastic selection algorithms, 37
Stretching frequencies, 191
Structural dissimilarity, 236
Structural diversity, 17
Structural parameters, 170
Structure, 142
Structure optimization, 143
Structure-activity relationship (SAR), 277
Structure-based drug design, 4, 32, 33, 217, 258, 277
Structure-based ligand optimization, 273
Structured sorbates, 194
Structures of materials, 144
Subset selection, 30
Substituted benzenes, 237
Substructural features, 8
Subtilisin, 253
Superconductors, 177
Surfaces, 177
Summation, 74
Summation functions, 75, 76, 89
Supercritical carbon dioxide solubilities, 93
Superdiffusivity effect, 194
Supervised classification problems, 109, 114
Supervised learning, 61, 62, 67, 70, 118
Supervised training, 61
Surface rearrangements, 199
Surfaces, 11, 12, 160, 173, 177, 197
Synapse, 56, 58
Synchronous mode, 63
Synthesis, 26
Synthetically efficient combinatorial library, 30
Systematic errors, 222, 235

T-cell activation, 269
Tautomerization, 225, 226, 227
Taylor series, 144, 154, 157, 163, 164
Temperature, 187
Temperature dependence of parameters, 189
Template, 29
Tertiary protein structure, 93
Test mode, 61, 87
Test patterns, 62
Test set error estimate, 125
Test sets, 62, 107, 111, 114, 125, 161, 168
Tetraalkylammonium ions, 236
Tetraalkylmethanes, 236
Tetrahydrofolate, 260
Thermal expansion coefficient, 200
Thermodynamic cycle, 226, 236, 238
Thermodynamic cycle perturbation (TCP), 224
Thermodynamic integration (TI), 218, 236
Thermodynamic perturbation theory, 243
Thermolysin, 248, 250, 285
Thermometer code, 105
Thread method, 281
Three-body augmented shell model, 181
Three-body potential, 196, 198
Three-body term, 199
Three-dimensional descriptors, 11, 35
Three-dimensional pharmacophore fingerprints, 16
Three-dimensional pharmacophore search, 14
Three-dimensional pharmacophores, 28
Three-dimensional QSAR, 277
Three-point pharmocophores, 11, 14
Three-layer network, 59, 121
Three-layer perceptron, 63
Threshold logic unit, 78
Threshold value, 117
Thymidylate synthase, 259, 260
Time series analysis, 70
Time series data, 108
TIP2P water models, 224
TIP3P water models, 224, 275, 287
TIP4P water models, 224, 238
TIPS potentials, 154
Tissue distribution, 232
Topological descriptors, 10
Topology-preserving map, 86
Topomeric descriptors, 12
Torsional energy, 221
Torsional motions, 142
Training a network, 108, 112
Training epoch, 61
Training mode, 87
Training pattern, 61
Training problems, 104
Training set construction, 108
Training sets, 61, 107, 111, 114, 161, 168
Training vector, 61
Transfer functions, 75, 77, 80, 89, 104, 109, 125
Transferability, 170, 172, 187
Transferable force field, 156
Transferable parameters, 161
Transformation, 74, 75, 103, 112
Transition state analog, 267
Translational motion, 5
Transport properties, 145, 176
Transport rates, 245
Triazoles, 228
Trichloroacetaldehyde, 235
Trimethoprim, 261
Trimethoxybenzene, 237
Triosephosphate isomerase (TPI), 257, 268
TRIPOS force field, 221
Trp analogs, 234
Trp-repressor, 266
True negative (TN) decision, 115
True negative ratio, 115
True positive (TP) decision, 115
True positive ratio, 115
Truncation errors, 221
Trypsin, 251
Tsar
, 128
Two-body potentials, 149, 196
Two-dimensional bit strings, 8, 28, 35
Two-dimensional connection table, 10
Two-dimensional descriptors, 38
Two-dimensional fingerprints, 16, 25, 35
Two-dimensional similarity, 17, 33
Two-dimensional string descriptors, 18, 35
Two-dimensional substructure searches, 17, 25
Two-layer perceptrons, 63

Unit, 57
Unit cell, 143, 184
United-atom force field, 255
Universal force field (UFF), 174, 175
Unlearning, 123
Unsupervised clustering problems, 109
Unsupervised competitive Kohonen learning, 99
Unsupervised learning, 62, 67, 68, 95, 100, 110
Urea, 233
Urey-Bradley term, 181
UV spectra, 92

Valence electrons, 152
Validation of descriptors, 16, 36
Validation set, 111, 125
Valine dipeptide, 237
Valinomycin, 248
van der Waals (VDW) parameters, 162, 175, 247
van der Waals interactions, 163
van der Waals term, 144
Variable orthgonalization, 106
Variable reduction, 106, 122
Variable selection, 106
Variable-response pairs, 70
Vector quantization, 91
Verlet algorithm, 279
Very large data sets, 10
Vibrational frequencies, 143, 188
Vibrational properties, 170
Vibrational spectroscopy, 154, 155, 187, 189, 194
Viral particles, 254
Virtual library, 30
Viscosity, 199
Vitreous borate, 199
Vitreous silica, 196, 197
Volume, 276

Water, 6, 7, 173, 193, 194, 223, 224, 233, 234, 236, 237, 244, 245, 247, 248, 279
Wavelet network, 100
Weighted product, 77
Weighted sum, 76
Weights, 58, 67, 68, 77, 81, 82, 83, 93, 112
Wellcome Registry
, 27
Widrow learning rule, 63
Widrow-Hoff rule, 83
Window errors, 225
Windows, 238, 249, 281, 287
Winning processing element, 80
World Drug Index database(WDI)
, 3, 16, 28, 36

X-ray diffraction data, 196
X-ray fluorescence, 94
X-ray structures, 6, 217, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 261, 262, 263, 265, 266, 267, 268, 269, 270, 271, 275, 276, 278, 279, 286
Xenobiotic oxidative metabolism, 260
Xenon, 192, 193

Yttrium barium copper oxide, 177, 179

Z-score, 104
Zeolite channels, 194
Zeolites, 158, 166, 167, 169, 180, 181, 185, 187, 190, 191, 193, 195, 201
Zero-point energy, 228
Zinc endopeptidase, 248
Zinc parameters, 258

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