REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 9 (1996)

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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A-74704, 23
Ab initio computations, 40, 132, 187
Abbott Laboratories, 11
Absolute shape descriptors, 196
Accessible molecular configurations, 200
ACE inhibitors, 10, 17
Acetylcholine receptor, 62
Acquired immunodeficiency syndrome (AIDS), 19
AESOP
, 7
Aglycon, 132
Agonists, 1, 3
Agouron Pharmaceuticals, 21
Alchemy
, 171
Alchemy II
, 178
Alchemy III
, 179
Aldosterone, 10
Alexander polynomial, 220
Algebraic topology, 226
Allopregnane, 40
Alpha protease inhibitor, 6
Alpha-amylase, 34, 35
Alpha-helix, 207, 208
Alzheimer's disease, 55
AM1, 21, 39, 40, 148
AMBER
, 7, 21, 37, 61, 110, 154
AMBER force field, 136, 146, 147, 148, 152, 165, 177, 179, 233
AMBER* force field, 179
Amino acid side chain, 5
Ammonium ion, 110
Analgesic effects, 51
Angiotensin I, 9
Angiotensin II, 9, 12
Angiotensin II antagonists, 10, 12, 15, 16
Angiotensin converting enzyme (ACE), 10, 12
Angiotensinogen, 9
Anharmonicity, 172
Anisometry, 198, 199, 200, 239
Annihilation of atoms, 100, 117
Anomeric effect, 131, 136, 143, 185
Anomeric stabilization, 132
Anomers, 137, 153
Antagonists, 1, 3
Antiaggregatory activity, 37
Antibacterial peptide, 61
Antibodies, 59
Antibody mimic, 59
Antipsychotic agents, 50
Aqueous solvation, 65, 146
Arthritis, 56
Aspartamine, 64
Asphericity, 199, 206, 239, 241, 242
Asthma, 56, 57
Atomic charges, 85, 154
Atomic polarizability, 85
Atomic radii, 222
Atomic replacement calculations, 111
Atrial natriuretic peptide, 17
Average conformation, 140
Average shape feature, 201
Averaged charge sets, 154

Bartell MUB2 force field, 177
Bartell MUB2' force field, 177
Basis set 4-31G, 137
Basis set 6-31G*, 132, 133, 135, 138, 149, 152, 154
Basis set 6-311G*, 40
Bending force constant, 172
Benzodiazepinedione, 38
Beta-carbolinones, 9
Beta-sheet conformation, 44, 61, 208
Beta-strand conformation, 33
Beta-turn conformation, 5, 35, 44, 52, 57, 58, 61, 62
Betti numbers, 226
Biasing potentials, 97, 106, 113
Bilayers, 230
Binding assays, 4
Binding conformation, 55
Binding epitope, 57
Bioactive conformations, 52, 57, 62
Bioavailability, 2
BIOGRAF
, 33
Biomembranes, 229, 230
Biphenyltetrazole antagonist, 15
Bitter taste, 64
Blood coagulation, 41
Blood group determinant, 149
Blood pressure, 10, 57
Boltzmann distribution, 85, 109, 141
Bond angle bending, 84, 172
Bond connectivity, 197
Bond dipoles, 144, 174
Bond stretching, 84, 171
Born equation, 108
Born-Oppenheimer approximation, 169, 196
Bound conformation, 4, 5
Boundary conditions, 109
Bovine pancreatic trypsin inhibitor (BPTI), 41
Boyd force field, 177, 178
Bradykinin (BK), 12, 57
Branched polymers, 206
Bronchitis, 6
Bronchoconstriction, 55, 57
Brookhaven Protein Data Bank
, 215
Buckingham potential, 137, 145
Buffered 14-7 function, 174
Butane, 134, 180

Cambridge Crystallographic Database
, 22, 35
Canonical curvatures, 225, 226
Canonical ensemble, 83, 106
Canonical partition function, 82, 86
Carbohydrate conformation, 131
Carbohydrate hydroxyls represented by extended atoms (CHEAT), 153, 157
Carbohydrate parameter sets, 147
Carbohydrate-protein complexes, 130
Carbohydrates, 129, 143, 150, 185
CAVEAT
, 35
Cbz, 7
CD4, 31
Cellular antiviral assay, 28
Center of mass, 202, 236
Central nervous system, 52
Cerius-2]
, 171, 179
CFF force field, 136, 147, 172
CFF91 force field, 148, 171, 172, 177, 179
CFF93 force field, 179
Characteristic ratio, 201, 208, 210
Charge groups, 119
CHARMm
, 58, 154
CHARMm force field, 136, 146, 147, 151, 153, 165, 171, 172, 173, 177
Chem3D Plus
, 175, 179
Chem3DPlus force field, 171, 177
Chemical and Engineering News
, xvii
Chemical graph theory, 205
Chem-X force field, 171, 172, 177
Chicago School of Pharmacy, 53
Chlorocyclohexane, 183
Chroman, 33
Ciba, 16
Clearance, 2
Clinical trials, 29, 46
Close packing, 224
Clustering analysis, 236
Clusters, 202
CNDO/2 calculations, 140
Cognitive disorders, 55
Collagen, 6
Collagenase, 33
Compactness, 200, 224, 237, 239
Compactness measures, 196
Complexity of entanglements, 213
Compositional features, 36
Compression functions, 171
Computational chemistry, xvi, 1, 5, 19, 64, 167
Computational co-crystallization, 25
Computational protocol, 149
Computer graphics, 167
Computer-assisted drug design, 238
Computer-assisted molecular design (CAMD), 64
Configurational averages, 208
Configurational equivalence, 221
Configurational space, 195
Conformational analyses, 58, 62, 65, 130, 141, 149
Conformational average, 209
Conformational changes, 200
Conformational energies, 167, 168, 177, 179
Conformational energy map, 17
Conformational features, 36
Conformational forcing, 106, 113
Conformational isomeric states, 105
Conformational scanning, 52
Conformational search method, 170
Conformational states, 4, 112, 119
Conformational transitions, 217
Congestive heart failure, 12
Conjugated systems, 175
Connectivity matrix, 205, 206
Connolly surface, 223
Consensus conformations, 37
Conservative system, 93
Constraint force, 105
Constraint work, 104
Constraints, 102, 118
Contact maps, 203
Contact matrices, 203
Continuum solvent model, 32
Control variable, 88, 119
Convexity, 227
Coordinate space probability, 83
Correlation analysis, 120
Correlation coefficient, 237
Correlation time, 142
COSMIC force field, 171, 172, 173, 177, 179
Coulomb potential energy function, 174
Coulombic interactions, 108
Coupling parameter, 90
Creation of atoms, 100, 117
Cross-terms, 175
Crown ethers, 112
Cryptands, 112
Crystal lattice energies, 145
Curvature elastic energy, 229
Curvature, 229
Curve crossings, 217
Cutoff distances, 108
CVFF force field, 136, 147, 171, 172, 172, 177, 179
Cyclic guanosine monophosphate (c-GMP), 50
Cyclic urea diol, 22
Cyclohexane, 182
Cyclophanes, 112
Cystic fibrosis, 6

De novo design, 2, 20
Deca(L-alanine), 234
Deca(L-glycine), 234
Degree of folding, 213
Degrees of freedom, 102
Degree of sampling, 106
Dendrimers, 206
DGEOM
, 37
Diagonal force fields, 175
Dielectric constant, 144, 146, 153
Dihedral angle, 207
Dihedral torsion, 84
Dihydroxyethane, 134
Dimethoxyethane, 134
Dimethoxymethane, 137, 149
Dimethylbutane, 180
Dipole moment, 85
Dipole tensor, 85
Discover
, 17, 25, 37, 59, 64
Dispersion forces, 183
Distance cutoffs, 203
Distance geometry, 37, 48, 65, 119, 130
Distance maps, 195, 202
Distance matrix, 202, 204, 235, 236, 239
Distance restraints, 157
Distance-dependent dielectric, 47, 174, 233
Distribution of interatomic distances, 202
Diuresis, 17
DNA, 112, 206, 217, 218, 219, 240
Docking, 7, 11, 22, 24, 25, 28, 41, 42, 66, 130
Dopamine receptor modulating peptide, 52
Double-wide sampling, 89
DREIDING force field, 33, 171, 172, 173, 177, 179
Drug discovery, 2, 5
Dual, 206
Dual topology description, 100, 117, 118
Dummy atom, 100, 101, 118
Dupont Merck Pharmaceuticals, 13, 22, 61
Dynamic shape, 217
Dynamic shape descriptors, 196, 197
Dynamic surface area, 235
Dynamically modified window technique, 99

Eccentricity, 199
ECEPP
, 46
ECEPP force field, 137
Edges, 228
Effective dielectric constant, 174
Effective pair potentials, 111
Elastic asymmetric bilayers, 230
Elastic surface behavior, 230
Elastic surfaces, 228
Elastic vesicles, 229
Elastin, 6
Electron density, 222, 237
Electronic polarization, 85, 110
Electrostatic decoupling, 118
Electrostatic functions, 174
Electrostatic interactions, 84, 140, 156, 169, 174
Electrostatic potentials, 228
Electrostatic term, 144
Eli Lilly and Company, 16
Endo-anomeric effect, 131
Endothelin-1 (ET-l), 42
End-to-end distance, 200, 209, 210
Energy, 83
Energy minimization, 170
Energy-weighted overlay, 60
Enkephalin, 51
Enkephalin mimetic, 52
Ensemble averaged NMR parameters, 141
Ensemble averages, 84, 86, 91, 109, 114, 150
Ensemble distance geometry, 44, 65
Ensemble molecular dynamics, 37, 65
Entanglements, 217
Enthalpies, 169, 175, 181
Entropic effects, 140
Entropy, 83, 94, 110, 168, 181
Enzyme inhibitors, 1
Enzyme substrates, 1
Enzyme surface, 8
Enzyme-bound conformation, 30
Enzyme-ligand bonding, 111
Enzymes, 1, 4, 111, 219
Equilibrium bond length, 171
Erabutoxin B, 62
Ergodic hypothesis, 208
Ermer-Lifson force field, 177
Error analysis, 109
Estimated parameters, 187
Euler-Poincaré characteristic, 225, 226, 230, 240
Exo-anomeric effect, 131, 136
Expectation value, 83
Explicit solvation, 148, 150, 153, 154, 155
Extended contact matrix, 203
External electric fields, 85

Fibrinogen, 36, 41
Fibrinogen receptor antagonists, 37, 39
Fibrinopeptide A, 41
Fibronectin, 40
Finite difference thermodynamic integration (FDTI), 93
Flexibility, 201, 217, 231, 235
Folding, 237, 240
Force field parameters, 99, 110, 169, 175
Force fields, 120, 130, 136, 146, 147, 167, 186
Force field AMBER, 136, 146, 147, 148, 152, 165, 177, 179, 233
Force field AMBER*, 179
Force field Bartell MUB2, 177
Force field Bartell MUB2', 177
Force field Boyd, 177, 178
Force field CHARMm, 136, 146, 147, 151, 153, 165, 171, 172, 173, 177
Force field CFF, 136, 147, 172
Force field CFF91, 148, 171, 172, 177, 179
Force field CFF93, 179
Force field Chem3DPlus, 171, 177
Force field Chem-X, 171, 172, 177
Force field COSMIC, 171, 172, 173, 177, 179
Force field CVFF, 136, 147, 171, 172, 173, 177, 179
Force field DREIDING, 33, 171, 172, 173, 177, 179
Force field ECEPP, 137
Force field Ermer-Lifson, 177
Force field GROMOS, 136, 146, 148
Force field MM2, 138, 143, 147, 170, 171, 172, 173, 175, 177, 179, 186
Force field MM2*, 170, 172, 174, 177, 179
Force field MM3, 143, 145, 146, 170, 172, 173, 175, 177, 179, 186
Force field MM3*, 170, 172, 174, 177, 179
Force field MMFF, 48, 171, 172, 177, 179, 186
Force field MMX, 171, 172, 179
Force field Osawa MM2', 177
Force field PCMODEL, 171, 177, 186
Force field PFOS, 139
Force field Rasmussen, 177
Force field Schleyer EAS, 177
Force field TRIPOS, 46, 136, 171, 172, 173, 177, 179
Force field TRIPOS (in Alchemy), 177
Force field UFF, 171, 172, 177, 179
Force field White-Bovill, 177, 178
Fourier series expansion, 172, 173
Fourier shape descriptors, 228
Fractal dimension, 210
Fractal index, 240
Fractal surface, 224
Fractal theory, 211
Fractality, 223, 224
Free energies of solvation, 102
Free energy, 81, 95, 106, 107, 110, 115
Free energy differences, 86, 87, 88, 89, 90, 94, 104
Free energy of activation, 90, 181
Free energy of hydration, 108, 110
Free energy perturbation (FEP), 9, 21, 66, 86, 88, 104, 114, 118, 131
Freely jointed chains, 201
Frenet-Serret formulas, 211
Frontier molecular orbital theory, 132

Gauche conformers, 134
Gauche interactions, 180
Gauss-Bonnet theorem, 230
Gaussian 90
, 40
Gaussian curvature, 229
Gaussian distribution, 202
Gene product, 18
Genentech, 37
General shape descriptor, 200
Generalized Born solvation model, 52
Genus, 225, 230
Geometrical descriptors, 195, 225
Geometry, 205
Geometry optimization, 170
Gepol
, 223
GESA, 138
Global descriptors, 208, 210, 240
Global energy minimum, 168, 170
Global topology, 240
Glucagon, 44
Glucopyranose, 146
Glucopyranoside, 155
Glucose, 45, 56
Glutathione reductase, 215, 216
GLYCAM parameters, 152, 154
Glycoprotein, 31
Glycoprotein complex GPIIb/IIIa, 36, 37, 39
Glycosidic linkages, 132, 137, 148, 152
G-protein-coupled receptor, 3
Grafted polymers, 206
Gramicidin-S, 61
Graph-theoretical descriptors, 228
Grid search, 138, 141
GROMOS
, 110, 154
GROMOS force field, 136, 146, 148
Grooves, 224
Growth hormone (hGH), 44, 47

Growth hormone releasing peptide 6 (GHRP-6), 47

Hamiltonian, 82, 84, 87, 93, 94, 103, 115
Hamiltonian coupling, 98
Hamiltonian space, 90
Hamiltonian time lag, 92, 114
Handedness index, 217
Hard-sphere exo-anomeric (HSEA) effect, 136, 137, 149, 153, 155
Harmonic potential, 100
HEAH algorithm, 139
Heats of formation, 143, 146, 170
Heats of sublimation, 145
Hebrew University, 56
Heisenberg principle, 196
Helfrich Hamiltonian, 229
Helical content, 207
Helix, 208
Helmholtz free energy, 83, 89, 106
Hessian, 225
HIV-1 protease, 11, 18, 19, 22, 24, 25, 26, 29
HIV-2, 19
Hoffmann-LaRoche, 21, 55, 56
Homeomorphic operations, 212
Homeomorphic transformations, 218
Homology groups, 226
Homology modeling, 111
Hormones, 1, 44, 47, 48
Host-guest affinity, 111
HSEL algorithm, 139
Human leukocyte elastase (HLE), 6
Hydration, 111
Hydrodynamic radius, 198
Hydrogen bonds, 6, 22, 29, 38, 134, 140, 145, 153, 154, 155, 169, 174, 207
Hydrophobic faces, 152
Hydrophobic interactions, 156
Hydrophobic residues, 7
HyperChem
, 233
Hyperglycemic activity, 62
Hypertension, 12
Hypertrehalosemic hormone (HTH), 61
Hypervariable domains, 59
Hypotension, 55
Hysteresis, 88, 92, 120

Immune system, 129
Immunomodulators, 1
Indentations, 224
Indinavir, 79
Inflammation, 57
Influenza viral enzyme, 59
Inhibitors, 3
Insight/Discover
, 171, 179
Insulin, 44
Interaction potential, 101
Interleukin 1alpha, 56
Isodensity surface, 226, 227
Isolated spin pair approximation (ISPA), 151
Isoproperty surfaces, 194
Isostere, 30
Isosteric replacements, 3, 33

Jaspamide, 62
Jeans formula, 174
JG-365, 19, 24
Jones polynomial, 221
Journal of Computational Chemistry
, v, vi, vii, viii, xiv, xix

Kinetic energy, 84
Kitaygorodsky potential, 137, 139
Knot invariants, 219
Knot polynomials, 195, 226, 240
Knot theory, 220
Knots, 218
Kratky-Porod model, 209
Kuhn's length, 200
Kurtosis, 208

L-366-948, 48
L-368,899, 48
L-685,434, 28
L-700,462, 39
L-735,524, 29
Lagrange undetermined multiplier technique, 103
Langevin dynamics, 157
Large-scale features, 193
Lecithin, 230
Lederle Laboratories, 31
Lennard-Jones 9-6 function, 174
Lennard-Jones 12-6 function, 173
Lennard-Jones interactions, 85, 101, 102
Leu-enkephalin, 17
Limetics, 3
Linking numbers, 219, 240
Links, 218
Lipophilic inhibitors, 7
Local curvatures, 224, 226, 227, 229
Local descriptors, 207
Local energy minimum, 170
Local fluctuations, 193
Local geometrical measures, 191, 240
Lone pairs, 143
Long-range interactions, 108
Loops, 218
Losartan, 14, 16, 79

MACCS 3D
, 22
MacMimic
, 178
MacroModel
, 11, 16, 28, 32, 33, 41, 45, 52, 57, 59, 62, 63, 171, 174, 175, 179
Macromolecular folding, 212
Macroscopic properties, 111
Major histocompatibility, class II, 31
Maltose, 146
Mannobioside, 150
Mannopyranoside, 155
Marion Merrell Dow Research Institute, 12, 17, 24
Matrix of inertia, 199
Maximized alignment, 238
Mayo Foundation, 50
McMaster University, 52
MDL 73,669, 24
MDL 100,173, 18
Medicinal chemistry, 1, 7, 8, 48
Membranes, 229
Merck Research Laboratories, 10, 25, 27, 28, 38, 47, 48
Metalloproteinases, 17
Metalloproteins, 220
Methoxytetrahydropyran, 132, 133, 144, 184
Methylcyclohexane, 182
Metric matrix, 202
Metropolis importance sampling, 85
Metropolis-Monte Carlo (MMC), 141
Micelles, 229
Microemulsions, 229, 230
MM2
, 37, 40, 45, 57, 63
MM2 force field, 138, 143, 147, 170, 171, 172, 173, 175, 177, 179, 186
MM2* force field, 170, 172, 174, 177, 179
MM2X
, 47
MM3 force field, 143, 145, 146, 170, 172, 173, 175, 177, 179, 186
MM3* force field, 170, 172, 174, 177, 179
MMFF force field, 48, 171, 172, 177, 179, 186
MMX force field, 171, 172, 179
MNDO, 138
Molecular compactness, 198
Molecular connectivity, 205
Molecular cross section graphs, 228
Molecular dynamics (MD), 7, 9, 25, 32, 37, 52, 57, 59, 60, 61, 63, 65, 66, 81, 84, 86, 87, 88, 91, 98, 103, 106, 114, 120, 136, 140, 146, 150, 155, 207, 232, 240
Molecular eccentricity, 199, 239
Molecular geometries, 168, 200
Molecular graphs, 195, 228
Molecular mechanics, 7, 24, 37, 62, 64, 65, 167
Molecular modeling, 5, 10, 12, 17, 23, 35, 36, 39, 40, 42, 45, 47, 56, 59, 61, 64, 129, 194
Molecular overlay, 13, 25, 43, 65
Molecular shape, 65, 191, 192, 211
Molecular similarity analysis, 205, 237, 240
Molecular simulations, 81, 84, 103, 120, 136, 140, 141, 232
Molecular size, 198
Molecular surface area, 239
Molecular surfaces, 222, 228
Molecular volume, 195, 223, 239
Molecular volume overlap, 55
Møller-Plesset second order (MP2), 134, 135, 136
Moments of inertia, 199, 237, 239, 241
Monash University, 59
Monoclonal antibody, 59
Monosaccharides, 129
Monte Carlo conformational search algorithms, 32, 41, 52, 65
Monte Carlo sampling, 232
Monte Carlo simulations, 85, 87, 88, 91, 94, 98, 114, 136, 140, 141
Morphine, 51, 52
Morse potential, 171, 145
MS
, 223
Multiconfiguration thermodynamic integration (MCTI), 91, 114
Multiple minima problem, 153
Multiple template approach (MTA), 50
Multiple-step thermodynamic perturbation (MSTP), 88
Mutation, 112
MVT-101, 24, 30

National Cancer Institute, 23
Natriuresis, 17
Nemesis
, 171, 178
Neurokinin A (NKA), 55
Neurokinin B (NKB), 55
Neuro-modulating agents, 1, 50
Neurotensin (NT), 50
Neurotoxic venom protein, 62
Neurotransmitters, 1
Neutral endopeptidase, 17
Neutron diffraction, 138
Newton's equations of motion, 101, 102, 103
Nicotinic acetylcholine receptor, 62
N
-methylacetamide, 185
NMR, 4, 34, 35, 36, 38, 41, 43, 45, 52, 57, 64, 111, 130, 134, 140, 142, 155, 157
NMR distance constraints, 44
Nomenclature, 66
Nonbonded interactions, 110, 132, 169
Nonbonded pair lists, 119
Nonpeptide inhibitors, 18, 20
Nonpeptidic compounds, 2
Nonphysical process, 101, 111
Normal modes, 102
Nuclear Overhauser effect (NOE), 48, 57, 138, 140, 151, 157
Nuclear spatial coordinates, 197
Nucleic acids, 218, 220

Oblate molecules, 199
Oxytocin, 48
Off-diagonal terms, 175
Off-lattice random walk, 203
Oligosaccharide-protein complexes, 135
Oligosaccharides, 129, 130, 140
One-dimensional descriptors, 202
One-dimensional (1D) model, 194
Opioid receptors, 51, 52
OPLS
, 110
OPTIMOL
, 25
Oral availability, 8, 12, 14, 15, 23
Order parameters, 233
Osawa MM2' force field, 177
Out-of-plane bending, 84
Overcrossing handedness, 220
Overcrossing probabilities, 212, 217, 218, 239
Overcrossing spectra, 214, 216
Overcrossings, 212
Overlapping phase space distributions, 118
Overlay model, 15

Pain, 55, 57
Pair potentials, 145
Parameter transferability, 145
Parameterization, 175
Partition coefficients, 111
Patents, 2
PCMODEL
, 174, 178, 179
PCMODEL force field, 171, 177, 186
PEF422 parameter set, 148
Peptidases, 2
Peptide mimetic design, 1, 3, 35, 64
Peptidic metabolite, 62
Peptidic recognition features, 5, 43
Peptidomimetics, 2, 40
Perhydroanthracene, 178
Periodic boundary conditions, 109, 146
Persistence length, 208
Perturbation configuration interaction using localized orbitals (PCILO), 139
PFOS force field, 139
Pharmacophore model, 5, 22, 45, 49, 55, 62, 65, 196
Phase shifts, 152
Phase space, 82, 87, 97, 106, 108, 109, 208
Phenylcyclohexane, 182
Phosphatidylinositol, 50
Physiological distribution, 2
pKa, 111
Platelet aggregation, 36, 37, 38, 40
Platelets, 36
Polarizable potential, 111
Polyglycine II helical strand, 208
Polymer conformations, 201
Polymer flexibility, 210
Polymer knots, 206
Polymer swelling, 240
Polymers, 193, 237
Polymethylene, 203
Polysaccharides, 129, 130
Porcine pancreatic elastase (PPE), 6
Potential energy functions, 169, 170
Potential of mean force, 90, 97, 106, 110, 113
Pre-size-and-shape space, 195
Principal moments of inertia, 199, 241
Probability distribution of overcrossings, 212
Probability function, 87
Prodrug, 18
Prolate molecules, 199
Protein families, 204
Protein shape, 208, 211
Protein-ligand recognition, 224
Proteins, 113, 224, 237
Pulmonary emphysema, 6
Pyranosides, 131, 132, 133, 143, 152
Pyridin-2-one, 7
Pyridopyrimidines, 9
Pyrimidone, 8
Pyrrolin-4-one, 10

QCPE, 223
QUANTA/CHARMm
, 47
Quantitative structure-activity relationships (QSAR), 205
Quantum similarity measures, 196, 238

Radial distribution function (RDF), 146, 195, 202
Radial distribution function for bonds, 206
Radius of gyration, 195, 198, 199, 200, 206, 208, 224, 239, 241, 243
Ramachandran diagram, 195, 207
Random incremental pulse search (RIPS), 52
Rasmussen force field, 177
Reaction coordinate, 106
Receptor-bound conformation, 43
Receptor-ligand complex, 96
Receptors, 1
Recognition elements, 4, 5, 24, 50, 55, 64, 65
Recommendations for simulations, 113
Red blood cells, 230
Reference bond angle, 172
Reference bond length, 171
Relative shape descriptors, 196, 235
Relative shape similarity, 237
Relaxation times, 110, 113, 119, 140
Renin, 10
Renin inhibitors, 10
Renin-angiotensin system, 9, 12
Restraint forces, 104
Restraint potentials, 97, 106
RGD mimics, 36, 39
Rheumatoid arthritis, 6
Rhinoviral infections, 57
Ribonuclease inhibitor, 214, 215
Ring puckering, 143
Ro 24-9975, 55
Ro 31-8959, 21, 25, 27, 28
Root-mean-square deviations, 196, 236
Rotating-frame Overhauser effect (ROE), 150
Rotational barriers, 178, 181
Rotational isomeric state, 105
Roughness, 228, 240

Saccharides, 142, 149
Sampling, 89, 109, 114
Sandoz, 46
SB 206343, 30
SC-52012, 39
Scaling, 192
Schleyer EAS force field, 177
Screens, 4
SEAL
, 47
Searle Research & Development, 39
Secretagogues, 6, 47
Seeing graphs, 228
Self-avoiding walk, 203
Self-entanglements, 212, 213, 239
Self-similarity, 211
Semiempirical quantum mechanical methods, 65
Sensitivity analysis, 110
Separation-shifted scaling, 101, 118
Sepsis, 57
Serine protease, 6, 41
SHAKE algorithm, 103, 105
Shape deformation, 229
Shape descriptors, 192, 194, 213, 239
Shape dynamics, 231, 232
Shape equations, 228
Shape fluctations, 221, 230
Shape group analysis, 226
Shape invariance region, 232
Shape persistence, 233
Shape similarity, 236
Shape space, 195
Shape stability, 222
Shape transitions, 240
Signal transduction, 3
Similarity analyses, 205
Simplicial homology theory, 226
Single step thermodynamic perturbation (SSTP), 88
Single topology description, 100, 118
Single-configuration thermodynamic integration (SCTI), 92, 110, 114
Size, 200, 239
Size exponent, 201
Size-and-shape space, 195
SK&F 66861, 43
SK&F 107260, 36
SK&F 108566, 15
Skewness, 208
Slow growth technique, 114
Small-scale features, 193
SmithKline Beecham Pharmaceuticals, 14, 29, 30, 36, 43
Smooth muscle proliferation, 43
Solubility, 2
Solute-solvent interactions, 148
Solvated oligosaccharides, 148
Solvation, 111, 130, 153
Solvation energies, 52
Solvation free energy differences, 22
Solvation shells, 202
Solvent-accessible surfaces, 223
Somatostatin (SRIF), 44
Somatostatin receptor, 45
SPC/E water model, 21
Spherical top molecules, 199
Sphericity, 223
Spontaneous curvature model, 231
Sprouting, 101, 118
SQUEAL
, 48
SRIF (Somatostatin), 44
State function, 90, 95, 115
Static shape descriptors, 196, 197
Statistical errors, 99, 109, 120
Statistical mechanics, 81
Stereoelectronic effects, 132
Steric energy, 169
Steric volume, 65
Sterling Winthrop Pharmaceuticals, 58
Steroid drugs, 40
Stochastic boundary conditions, 109
Stretching force constant, 171
Structural stability, 232
Structure-activity relationship (SAR), 6, 14, 17, 25, 36, 38, 46, 48, 50
Structure-based design, 7, 10
Substance P (SP), 55
Sucrose, 64, 138
Sulfolanes, 27
Supercoiling, 217
Surface area, 223
Surface descriptors, 235
Surface geometry, 225
Sweet-tasting compounds, 64
Switching functions, 93
Swollen polymer, 204
SYBYL
, 14, 20, 23, 171
Syntex Research, 20
Systematic errors, 88, 92, 109

T lymphocytes, 31
Tachykinins, 55
Takeda Chemical Industries, 12
Taste molecules, 64
Tendamistat, 34, 35
Texas A&M University, 62
Therapeutic intervention, 1, 10, 47, 111
Thermal fluctuations, 230
Thermodynamic cycle, 81, 95, 96, 111
Thermodynamic cycle perturbation (TCP), 21, 86, 88, 104, 114, 118
Thermodynamic integration, 89, 90, 91, 92, 94, 118
Thermodynamic state function, 106
Thermolysin, 17, 32
Theta temperature, 201
Three-dimensional database search, 22
Three-dimensional (3D) model, 194
Thrombin, 41
Thrombin-hirudin complex, 41
Thrombus, 36
Thyrotropin-releasing hormone (TRH), 54
Thyrotropin-stimulating hormone, 54
Time averages, 208
TIP3P water model, 148
Topological descriptors, 195, 225
Topological dimensionality, 194, 211
Topological invariants, 218, 219, 230
Topology, 218
Torsion of a strand, 219
Torsional angles, 132, 135, 138, 150, 169
Torsional potential functions, 137, 173
Total energy, 147
Transition state analogue, 11
Trefoil knot, 220
Trimethyl-isopropylbenzene, 181
Trineopentylbenzene, 183, 184
TRIPOS force field, 46, 136, 171, 172, 173, 177, 179
Truncated surface, 226
Trypsin, 41
Turkey ovomucoid inhibitor (TOMI), 6
Twin range cutoff, 119
Twist, 219, 239
Two-dimensional descriptors, 202
Two-dimensional (2D) model, 194

Umbrella potential, 110
Umbrella sampling, 97
Universal force field (UFF), 171, 172, 177, 179
University of California, Berkeley, 32, 35
University of California, San Diego, 64
University of Illinois at Chicago, 31, 41, 51, 57, 59, 62
University of Minnesota, 52
University of Pennsylvania, 10, 28, 40, 45, 59
University of Texas at Austin, 33
University of Washington, 52
Unknotted loop, 220
Uterine contractions, 48

Valsartan, 16
van der Waals functions, 137, 139, 173
van der Waals graphs, 228
van der Waals interactions, 84, 156, 169, 183
van der Waals surface, 192, 223, 224, 227
Vasoconstriction, 10, 43
Vassiliev numbers, 221
Vertices, 228
Vesicles, 201, 229
Vibrational frequencies, 143, 175
Virtual conformation, 130, 140, 151, 157
Virtual knots, 220
Vitronectin, 40
Volume, 222, 223

Weizmann Institute of Science, 40
White-Bovill force field, 177, 178
World distribution of chemistry publications, xviii
World distribution of computational chemistry publications, xiv
World distribution of science publications, xvii
Wormlike polymer, 209
Writhing number, 217, 219, 239

X-ray crystal structure, 4, 6, 7, 9, 10, 17, 19, 21, 24, 25, 27, 28, 29, 30, 31, 32, 36, 41, 42, 54, 57, 60, 62, 64, 111, 134, 138
Xylose, 46

Yeast hexokinase B, 214, 215, 216

Zeneca Pharmaceuticals, 6
Zero-dimensional descriptors, 200
Zero-dimensional (0D) model, 194

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