REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 3 (1992)

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, 143
ACES II, 239
Acetanilide, 183
Acetophenetidin, 183
Acute lethal dose (LD50), 173, 174
Acyl carrier protein, 154
Adaptive Importance Sampling Monte Carlo, 110, 114
Aflatoxin B1, 201
Ah
receptor, 188, 191, 195
ALADDIN, 245
L-Alanine, 80
ALCHEMYII, 242
Alchemy III, 226
Alcohols, 202
Aliphatic amines, 198
All-atom force field, 146
Alpha helix, 92, 94, 97, 98, 102
Alpha/alpha packing, 98
Alpha-amino isobutyric acid (Aib), 96
Alpha/beta packing, 98
Alpha-carbon, 76
Alpha-helical conformations, 84
Alpha-helix sense, 96
Alpha-lactalbumin, 127
AMBER, 82, 84, 86, 233
Ames test, 176, 199, 204
AMPAC, 230, 236
Amphetamine, 205
AMSOL, 236
Anharmonicity, 89, 129
Aniline mustards, 197
Animal tests, 175
Annealing protocol, 162
Antiparallel beta sheets, 98
Apex, 235
Approximate Newton search direction, 43
Area/depth parameter, 191
Arene oxides, 202
Argus, 239
Armijo and Goldstein criterion, 25
Aromatase, 185
Aromatic acids, 202
Aromatic amines, 196, 202
Aromatic hydrocarbons, 198, 202
Aromatics, 202
Array processors, 94
Asparagine, 101
Aspartic acid, 101
ASTERIX, 239
ATOM, 229
Atom-centered pair potentials, 83
ATOMPLUS, 229
ATOMSCF, 242
Automated data analysis by pattern recognition techniques (ADAPT), 178, 203, 206, 210
Automatic differentiation, 29
AUTONOM, 229
Average conformation, 114
Average solution structure, 153
Avian pancreatic polypeptide, 128, 129
AVS ChemistryViewer, 237

Ball & Stick, 230
Basic descent, 21
Basic pancreatic trypsin inhibitor (BPTI), 150
Basic linear algebra subroutines (BLAS), 63
Benoxaprofen, 195, 197
Benzanthracenes, 196
Benzimidazoles, 196
Benzo[a]pyrene, 202
Benzoquinolines, 202
Beta barrels, 98
Beta sheet, 94, 96, 97, 98, 126
Beta turns, 126
Beta-alpha-beta crossover packing, 98
Beta/beta packing, 98
Beta-proteins, 150
BIGSTRN3, 236
Bioavailability, 181
BIOGRAF, 180, 237
Biologically active form, 103
BLDKIT, 243
Blocked amino acid residue, 81
Boltzmann distribution, 110
Boltzmann-averaged conformation, 74
BOSS, 238
Botulinum toxin, 174
Bovine pancreatic trypsin inhibitor (BPTI), 91, 123, 127
Brookhaven Protein Data Bank, 128
Brownian dynamics, 93
Broyden-Fletcher-Goldfarb-Shannon (BFGS) formula, 41, 59, 63
Broyden's quasi-Newton method, 40
Buildup technique, 17, 102, 104, 123, 128
Buildup with limited constraints, 123
Butane, 16, 17
t-Butyl alcohol, 205
[[gamma]]-Butyrolactone, 205

CAChe Work System, 226
CADPAC, 240
Cambridge Structural Database, 245, 246
CAMELEON, 244
Camphor, 188
CAMSEQ/M, 226
Carbon monoxide, 173
Cardiotoxicity, 174
Cartesian coordinate system, 76, 78
CASE (computer-automated structure evaluation), 178, 203, 210
Catalyst, 233
CAVEAT, 244
Cayley-Menger determinant, 115
Cerius, 237
CHAIN, 247
Chance correlations, 179
CHARMm, 180, 237
CHARMM, 82, 84, 86, 233, 237
CHELPG, 240
Chem3D Plus, 227
ChemCad+, 227
ChemDBS-3D, 244
Chemical carcinogens, 187
Chemlab, 180
chemVISION, 231
Chem-X, 180, 227, 234, 244
Chiral errors, 164
Chirality, 148, 149
Chloracetic acid, 205
Chloramine, 205
Chlorobenzyl aspartates, 95
Cholesky factorization, 45
Chrysenes, 196
Cis
peptide bonds, 85, 102
Classic Newton, 47, 48
CLOGP, 209, 245
Cluster analysis, 178
CNDO/2 method, 201
CNINDO, 236
COBRA, 244
Coiled-coil packing of helices, 98
Collagen, 104, 123
COLUMBUS, 240
Comparative Molecular Field Analysis (COMFA) 180, 238
Complete metrization, 163
Composer, 238
Computer-optimized molecular parametric analysis of chemical toxicity (COMPACT), 180, 181, 190, 191, 193, 195, 199, 204, 206, 210
Computer programs
3D Dictionary, 244
ACES II, 239
ALADDIN, 245
Alchemy III, 226
ALCHEMYII, 242
AMBER, 82, 84, 86, 233
AMPAC, 230, 236
AMSOL, 236
Apex, 235
Argus, 239
ASTERIX, 239
ATOM, 229
ATOMPLUS, 229
ATOMSCF, 242
AUTONOM, 229
AVS ChemistryViewer, 237
Ball & Stick, 230
BIGSTRN3, 236
BIOGRAF, 180, 237
BLDKIT, 243
BOSS, 238
CAChe Work System, 226
CADPAC, 240
CAMELEON, 244
CAMSEQ/M, 226
CASE, 178, 203, 210
Catalyst, 233
CAVEAT, 244
Cerius, 237
CHAIN, 247
CHARMM, 82, 84, 86, 180, 233
CHELPG, 240
Chem-X, 180, 227, 234, 244
Chem3D Plus, 227
ChemCad+, 227
ChemDBS-3D, 244
Chemlab, 180
chemVISION, 231
CLOGP, 209, 245
CNINDO, 236
COBRA, 244
COLUMBUS, 240
COMFA, 180, 238
Composer, 238
CONCORD, 238, 246
CONECT, 243
CONMIN, 50
CONSTRICTOR, 244
Converter, 235
COSMIC, 180
DADAS, 150
DAYMENUS, 244
Delphi, 234
DEREK, 180, 181, 204, 206, 210
Desktop Molecular Modeller, 227
DGEOM, 236
DIANA, 151, 157
DISCOVER, 82, 86
DISGEO, 148, 236
DISMAN, 150
DMol, 241
DNA/RNA Builder, 232
DOCK, 246
DRUGIDEA, 181
ECEPP/2, 76, 79, 82, 83, 84, 115, 118, 120
ECEPP/3, 84
EUREKA, 244
FANTOM, 161
FISIPL, 243
FITIT, 246
FORTICON8, 230, 236
FRODO, 246
GAMESS, 241
Gauss2, 229
Gaussian, 241
GRADSCF, 242
GRID, 247
GROMOS, 234
GSTAT, 245
H2ION, 229
HAMOG, 228
HAZARDEXPERT, 177, 180, 181, 204, 206, 211
HMO, 230
HONDO, 242
HyperChem, 228
Insight/Discover, 180, 234
ISIS, 245
Kekulé, 231
KGNGRAF, 242
KGNMOL, 242
Kinemage, 231
LAPACK, 64
LHASA, 180
Ludi, 235
MacImdad, 231
MacMimic, 228
MacroModel, 235
MAD, 235
MELD, 242
METABOLEXPERT, 180, 231
MicroChem, 228
MidasPlus, 247
MM2, 83, 230, 236
MM3, 235, 236
MNDO, 236
MNDO90, 243
MNDOC, 236
MOBY, 229
MODEL, 235
MOLCONN-X, 232
Molecular Silverware, 238
Molecules, 232
MOLIDEA, 180, 181
MOPAC, 230, 236
NAMOD, 230
NanoVision, 232
NEMESIS, 229
NITRO, 238
NMR TRIAD, 238
NMRchitect, 235
NMRgraf, 237
N.N.Charge, 232
OpenMolecule, 247
PCILO3, 236
PCMODEL, 229
Pimms, 244
PLUTO, 245
POLYGRAF, 237
Polymer, 235
POLYRATE, 236
POSSUM, 246
PRO-EXPLORE, 236
Pro-log P, 181, 209
Prometheus, 237
PROPHET, 237
PRO-QUANTUM, 236
PROTE, 246
Protein Predictor, 232
PSI88, 242
Python, 244
QSPR-Polymer, 237
Quanta, 180
QUANTA/CHARMm, 237
QUEST, 245
RECEPTOR, 238
RTECS, 210
SAVOL2, 245
Serratus, 244
SIMCA-R, 178, 247
Sketcher, 235
SPARTAN, 242
SPASMS, 233
STERIMOL, 230
STN EXPRESS, 230
SUMSL, 93
SYBYL, 180, 238
SYBYL/3DB, 246
TNPACK, 50
TOPDRAW, 233
TOPKAT, 177, 179, 203, 206, 210, 232
TOPMOST, 232
Toxline, 210
UniChem, 243
WHAT IF, 238
X-PLOR, 237
Yak, 239
Yeti, 239
ZINDO, 243
CONCORD, 238, 246
Condition number, 30
Conditional free energy, 114
Conditions at minima, 5
CONECT, 243
Configurational entropy, 92
Conformational entropy, 92
Conformational free energy, 92
Conformational space, 144, 154, 163
Conjugate direction, 32
Conjugate gradient, 30, 59, 63, 93
CONMIN, 50
CONSTRICTOR, 244
Contraction in dimensionality, 115
Convergence, 28, 42, 150
Convergence bounds, 32
Convergence characterization, 28
Convergence criteria, 26
Convergence order, 28
Convergence rate, 30
Convergence ratio, 28, 30
Convergence test, 27
Converter, 235
Cooling schedule, 121
Coordinate descent methods, 29
Correlated distances, 148
COSMIC, 180
Coulomb's law, 89
Coumarins, 193, 195, 196
Coupling constant, 157
Covalent restraints, 144, 149
Crystal packing interactions, 103
Cyclohexaglycyl, 80
Cyclosporin A, 151
Cytochromes P450, 176, 182, 184

3D Dictionary, 244
DADAS, 150
Databases, 230, 243
DAYMENUS, 244
Dealkylation, 183
Decaglycine, 92
Decay constant, 155
Deformation of the potential energy space, 116
Deformed potential surface, 120
Degrees of freedom, 92
Dehalogenation, 183
Delphi, 234
Delta-endotoxin, 173
Deoxycytidine, 55
DEREK (deductive estimation of risk from existing knowledge), 180, 181, 204, 206, 210
Descent directions, 21, 30
Descent methods, 18
Descent structure of local methods, 20
Descriptor variables, 179
Desktop Molecular Modeller, 227
Deterministic global algorithm, 19
Deterministic methods, 18
DGEOM, 236
2,4-Diaminophenol, 205
DIANA, 151, 157
Dibenz[a,h]anthracene, 192
2,3-Dibromo-1-propanol, 205
Dielectric constant, 90
Diffusion equation, 116
Diffusion equation method (DEM), 118, 120
Dihedral angle restraints, 157
Dihedral angle space, 118
Dihedral angles, 80, 150
3,4-Dihydrocoumarin, 205
3,3'-Dimethylbenzidine, 205
Diol epoxides, 202
Diphenylhydantoin, 204
Dipolar interactions, 152, 154
Dipolar relaxation, 155
Dipole moment, 202
DISCOVER, 82, 86
Discrete conformations, 153
Discrete Newton, 35, 38
Discriminant analysis, 178
DISGEO, 148, 236
DISMAN, 150
Dissimilarity, 164
Distance constraint potential, 152
Distance constraints, 127
Distance geometry, 115, 144
Distance matrix, 147, 163
Distance matrix error, 164
Distance restraints, 145, 152, 153, 155
Distance-dependent function, 90
DMol, 241
DNA, 6, 18
DNA/RNA Builder, 232
DOCK, 246
Dose-response curves, 208
Drug design, 103
DRUGIDEA, 181
Dynamical simulated annealing, 159

ECEPP/2, 84, 118
ECEPP/3, 84
Electrostatic field, 90
Electrostatic isopotential (EIP), 201
Electrostatic potential energies, 201
Electrostatically driven Monte Carlo (EDMC), 110, 120
Elongation factor, 193
Embed algorithm, 147, 148, 149
Empirical Conformational Energy Program for Peptides (ECEPP), 76, 79, 82, 83, 115, 120
Empirical hydration models, 91
End groups, 76, 77
Energy embedding algorithm, 160
Enkephalin, 103, 108
Ensemble, 74
Ensemble average, 153, 154
Environmental Protection Agency, 207
Epoxidation, 183
Epoxide hydrase, 201
Epoxides, 202
Ethyl alcohol, 174
Ethylene glycol, 205
Euclidean norm, 27
EUREKA, 244

FANTOM, 161
Fast particle methods, 16
Ferrous sulfate, 174
Fibrous proteins, 104, 120, 123
FISIPL, 243
FITIT, 246
Fletcher-Reeves (FR) formula, 34
Flexible geometry, 86
Folded structures, 75
Food and Drug Administration structural alerts, 207
Force field, 161
FORTICON8, 230, 236
Four-dimensional coordinates, 149
Fourier-Poisson integral, 118
Free-volume method, 93
Friction term, 160
FRODO, 246
Frontier orbital energies, 193
Frontier orbitals, 209
Full-memory quasi-Newton methods, 42, 47, 48

GAMESS, 241
Gauss2, 229
Gaussian, 241
Geometry, 81
Global minimum, 75, 84, 94, 102, 116, 118, 121, 123, 160
Global minimum function, 28
Global optimization methods, 18
Globoside, 153
Globular proteins, 104, 123
Glycine, 150
Gradient, 3
Gradient methods, 30
Gradient vector, 4, 12
GRADSCF, 242
Gramicidin S, 80, 103, 104, 105
Grand challenge, 63
GRID, 247
GROMOS, 234
GSTAT, 245

H2ION, 229
Hairpin, 92
Hamiltonian operator, 118
HAMOG, 228
Hard-sphere potential, 81, 82, 86
Harmonic function, 89
HAZARDEXPERT, 177, 180, 181, 204, 206, 211
Helix breaking, 99
Helix stability, 99
Helix-coil transition, 98, 126
Hemicholinium-3, 174
Hemoproteins, 188
Hessian, 3, 4, 5, 38, 46, 47, 63
Hestenes-Stiefel (HS) formula, 34
Hexapeptide, 126
Higher-dimensional Euclidean space, 160
Highest occupied molecular orbitals, 193
HMO, 230
Homologous structural fragments, 151
Homology, 127
Homology matching, 190
HONDO, 242
Hückel method, 201
Human leukocyte interferon, 123
Hydration, 129
Hydrogen bonds, 62, 84, 103
Hydrophobic interactions, 98, 100, 190
Hydrophobic parameters, 209
Hydrophobicity, 177
4-Hydroxyacetanilide, 205
Hydroxylation, 183
HyperChem, 228
Hyperplane, 4

Increase in Dimensionality, 115
Indefinite matrix, 12
Initial structures, 146, 151
Insight/Discover, 180, 234
Intensity, 152
Interchain interactions, 104
ISIS, 245

Kekulé, 231
Ketoconazole, 185
KGNGRAF, 242
KGNMOL, 242
Kinemage, 231
K-L theory of carcinogenesis, 201
Knowledge-based systems, 179

Lac
repressor headpiece, 159
Langevin equation, 160
LAPACK, 64
Laplacian, 117
Lennard-Jones 6-12 potential, 82
LHASA (logic and heuristics applied to synthetic analysis), 180
Liberational entropy, 92
Limited-memory Broyden-Fletcher-Goldfarb-Shannon formula (LM-BFGS), 42, 59
Limited-memory quasi-Newton (LMQN), 35, 41, 47, 48
Line search, 21, 22, 34
Linear conjugate gradient, 32
Linear preconditioning conjugate method, 43
Linearized embedding, 149
Local algorithm, 19
Local minima, 2, 102, 110, 122, 149, 158
Local minimization algorithms, 20
Local optimization methods, 18
Local preconditioner, 45
Local terms, 33
Locally acceptable segments, 151
Log P, 177, 181, 190, 201, 209
Long-range interactions, 16, 87, 149
Loop segments, 79
Lothionein, 150
Lower dimensional spaces, 160
Lower distance bounds, 147, 150
Lowest empty molecular orbitals, 193
Ludi, 235
Lysozyme, 127

MacImdad, 231
MacMimic, 228
MacroModel, 235
Macromolecular modeling, 90
MAD, 235
Manual model building, 151
Many-body interactions, 129
Mathematical notation, 3
Matrix density, 4
Mean-field theory, 118, 120
MELD, 242
Memory function, 155
METABOLEXPERT, 180, 231
Metabolism, 181
Metabolite "tree", 181
Metal toxicity, 203
Met-enkephalin, 102, 104, 109, 113, 115, 118, 119, 123, 124
Methoxyflurane, 183
Methyl bromide, 205
Metric matrix method, 147, 150, 163
Metropolis criterion, 108, 110
Metropolis Monte Carlo, 93, 110, 114, 121
MicroChem, 228
MidasPlus, 247
Minicomputers, 233
Minimization methods, 93
Minima, 4, 5, 10
Minimum-energy point, 85, 87
Mixed function oxidases, 182
Mixing time, 165
MM2, 83, 230, 236
MM3, 235, 236
MNDO, 236
MNDO90, 243
MNDOC, 236
MOBY, 229
MODEL, 235
Modified Cholesky (MC), 46
Modified Cholesky factorization, 47, 63
Modified Newton, 37
MOLCONN-X, 232
Molecular connectivity, 178
Molecular diameter, 199
Molecular dimensions, 180, 209
Molecular dynamics, 17, 91, 93, 158
Molecular dynamics trajectory, 154
Molecular electrostatic potential, 209
Molecular force field, 144
Molecular fragment, 178
Molecular graphics, 230, 246
Molecular mechanics, 16, 45
Molecular modeling, 143, 223, 233
Molecular orbital calculations, 200
Molecular Silverware, 238
Molecules, 232
MOLIDEA, 180, 181
Mono-oxygenases, 182
Monte Carlo, 91, 119, 121, 161
Monte Carlo plus minimization (MCM), 106, 110, 120
Monte Carlo recursion, 93
MOPAC, 230, 236
Morphine sulfate, 174
Multidimensional phase space, 2
Multiple instructions multiple data (MIMD), 63
Multiple regression analysis (MRA), 177
Multiple-minima problem, 16, 102, 104, 120
Multivariate property space, 128

Nabla operator, 156
N-acetylglycyl-N'-methyl amide, 84, 87
N-acetylglycyl-N'-methylalanine amide, 86
NAMOD, 230
NanoVision, 232
2-Naphthylamine, 183
Naphthylene, 183, 205
National Toxicology Program (NTP), 199
Native conformation, 75
Negative-definite matrix, 4, 12
NEMESIS, 229
Neurotoxicity, 174
Neurotransmitter receptors, 174
Newton direction, 36
Newton equation, 36, 50
Newton methods, 35
Newton-Raphson, 35
Newton's equations of motion, 159
Nicotine, 174
Nitriles, 196
NITRO, 238
p
-Nitroaniline, 205
o
-Nitroanisole, 205
Nitroarenes, 202
p
-Nitrobenzoic acid, 205
p
-Nitrophenol, 205
Nitrosamines, 196, 202
Nitrosoureas, 197
NMR distance constraints, 123
N.N.Charge, 232
NMR TRIAD, 238
NMRchitect, 235
NMRgraf, 237
NOESY cross-peaks, 157
Nonbonded energy, 84
Nonderivative methods, 29
Nonhelical conformations, 99
Nonlinear conjugate gradient algorithms, 26, 34, 39, 42, 47, 48
Nonlocal terms, 33
Non-Newtonian dynamics, 160
Nuclear magnetic resonance (NMR), 143
Nuclear magnetic resonance restraints, 149
Nuclear Overhauser enhancement (NOE), 144, 152, 155, 156
Nucleic acids, 17

Objective function, 2, 36, 43, 51, 115
Octanol/water partition coefficient, 209
Oligonucleotide, 155
Oligopeptides, 73, 87, 120
Omega-helical form, 102
OpenMolecule, 247
Optimization, 1

Parallel beta sheets, 98
Parallelism, 94, 129
Partial metrization, 163
Partition coefficient, 177, 209
Partition function, 74, 110, 111
Pattern recognition, 177
Pattern-recognition importance sampling minimization (PRISM), 128
PCBs, 196, 202
PCILO3, 236
PCMODEL, 229
PEACS, 160
Penalty function, 115, 144, 150, 152, 156, 157
Pentachloroanisole, 205
Pentobarbital, 183
Personal computers, 226
Phenobarbital, 184, 192
Phenobarbital sodium, 174
Phenyl aziridines, 197
Phenytoins, 198
Phi/psi map, 81, 84, 88, 114, 128
Picrotoxin, 174
Pimms, 244
pKa, 181
PLUTO, 245
Poisson-Boltzmann equation, 90
Polak-Ribiere (PR) formula, 34
Polarizability, 202
Polarization, 129
Polyamino acids, 96
Polycyclic aromatic hydrocarbons (PAHs), 184, 190, 193, 199, 200, 202
Poly(Gly-Pro-Pro), 106, 107
POLYGRAF, 237
Poly-L-alanine, 94, 95, 111, 112
Poly-L-proline, 85
Poly-L-valine, 96, 101
Polymer, 235
Polynucleotides, 17
Polypeptides, 17, 73, 121
POLYRATE, 236
Positive semidefinite matrix, 4, 12
Positive-definite matrix, 4, 12
POSSUM, 246
Potential energy function, 16, 82, 86
Potential energy minimization, 17
Powell's method, 29
Precision, 17
Preconditioning, 32, 42
Preconditioning conjugate gradient (PCG) method, 33, 44
Pregnenolone, 184
Principal components analysis (PCA), 178
Probability density, 164
PRO-EXPLORE, 236
PROFILE method, 151
Pro-log P, 181, 209
Promethazine, 205
Prometheus, 237
PROPHET, 237
PRO-QUANTUM, 236
PROTE, 246
Protein backbone, 148
Protein data bank, 145
Protein folding, 93
Protein Predictor, 232
Proteins, 74, 87, 121, 123
Pseudo parameter, 55
Pseudo-atoms, 145
Pseudo-energy force constants, 162
Pseudo-energy term, 145, 153, 161
PSI88, 242
Python, 244

QCPE, 230
QSPR-Polymer, 237
Quadratic convex function, 28
Quadratic truncation (QT), 44
Quanta, 180
QUANTA/CHARMm, 237
Quantitative structure-activity relationships (QSARs), 176
Quasi-Newton (QN), 35, 38
QUEST, 245

R factor, 165
Rank 1 update, 40
Rank 2 update, 41
RECEPTOR, 238
Receptor, 103
Redox potential, 203
Regularity constraint, 73
Relative entropy, 92
Residual test (RT), 43
Residue geometry, 76
Resorcinol, 205
Restart vector, 35
Restrained molecular dynamics, 144
Right-handed alpha helix, 110
Ring closure with symmetry, 80
Ring closure without symmetry, 79
Root-mean-square deviation, 126
Rosenbrock minimization, 51, 55
Rotational embedding algorithm, 160
Rotational entropy, 102
RTECS, 210

Saddle point, 7, 10
Sampling bias, 163
Sampling properties, 149, 155
SAVOL2, 245
Search direction, 21, 42
Search vector, 18, 21, 32, 36, 50
Secant approximation, 39
Secant unconstrained minimization solver (SUMSL), 93
Self-consistent electric field (SCEF), 106, 110
Self-consistent multitorsional field (SCMTF), 118
Serine, 100
Serratus, 244
Shape parameters, 192
Sherman-Morrison-Woodbury formula, 41
Short-range interactions, 87, 126, 149
Silk, 123
SIMCA-R, 247
Simulated annealing, 17, 18, 115, 121, 123, 159
Single instruction multiple data streams (SIMD), 63
Sketcher, 235
SNIFR, 160
Sodium chloride, 174
Soft, independent modeling of class analogy (SIMCA), 178
Solvation, 74, 91
Solvent parameters, 209
Solvent-accessible surface area, 91
Soret band, 188
Sparse factorization techniques, 45
Sparse matrix, 4
SPARTAN, 242
SPASMS (San Francisco Package of Applications for the Simulation of Molecular Systems), 233
Spin diffusion, 155
Squash trypsin inhibitor, 156
Stationary point, 7
Statistical coil, 92
Steepest descent (SD), 30, 54, 93
Step length, 21, 32, 37
Steric map, 83
STERIMOL, 230
Steroid hormones, 182
Steroids, 195, 196, 199
STN EXPRESS, 230
Stochastic dynamics, 159
Stochastic global algorithm, 19
Stochastic global optimization, 17, 18
Strict local minimum, 21
Structural descriptors, 176
Structure-toxicity models, 203
Strychnine sulfate, 174
Substituent constants, 177
Substructural fragments, 181
Substructure embedding, 148, 163
Supercomputers, 233
Superdelocalizability, 201
Superminicomputers, 233
SYBYL, 180, 238
SYBYL/3DB, 246
Symmetric matrix, 4
Symmetric rank 1 update (SR1), 40
Systematic biases, 163
Systematic errors, 163

Tangent vector, 12
Taylor expansion, 5, 9
TCDDs, 174, 196, 202
Tendamistat, 150
Testosterone, 186
Tetrodotoxin, 174
Theophylline, 205
Thermodynamic integration, 93
Thermodynamic perturbation theory, 93
Three-dimensional NMR, 156
Threonine, 100
Time-averaged distance restraints, 154
TNPACK, 50
TOPDRAW, 233
TOPKAT, 177, 179, 203, 206, 210, 232
TOPMOST, 232
Toxic endpoint, 207
Toxic radicals, 203
Toxic segments, 181
Toxicity evaluation, 176
Toxicity predictions, 205
Toxicity rating, 174
Toxicity tests, 175
Toxicity, 208
Toxicology, 173
Toxline, 210
Trans
peptide bond, 79, 85, 102
Trial distance matrix, 148
Triamterene, 205
Triangle smoothing, 147
1,2,3-Trichloropropane, 205
Tricresyl phosphate, 205
Truncated Newton (TN), 35, 43, 45, 46, 47, 48, 50, 59
Trust radius, 22
Trust region, 21, 34
d
-Tubocurarine, 174
Two-dimensional NMR, 103, 144

Umbrella sampling, 93
UniChem, 243
United-atom, 90, 146
United-residue, 90
Upper distance bounds, 147, 150
UV absorption, 188

van der Waals radii, 150
Variable metric, 35
Variable target function method, 149, 163
Vibrational entropy, 74, 75
Vicinal protons, 157
Virtual atom, 146
Virtual bonds, 93

Water, 90, 99
Water clusters, 61
Water-accessible volume, 91
WHAT IF, 238
Workstations, 233

Xenobiotics, 182
X-PLOR, 237
X-ray crystallography, 145, 188

Yak, 239
Yale Sparse Matrix Package (YSMP), 45, 50, 55
Yeti, 239

Zimm-Bragg parameters, 98
ZINDO, 243

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