REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 17 (2001)

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*-algorithm, 20
Absolute gravity, 218, 219
Absorption, distribution, metabolism, and excretion (elimination) (ADME), 38, 221
Accelrys, viii
Accessible surface area, 25
Acid dissociation, 234
ADAM
, 7
AMBER
, 26
AMBER force field, 14, 15, 18, 19, 81
American Chemical Society (ACS), v
Amphiphile, 231
Anchor fragments, 12, 14
Angular momentum, 100, 102, 103, 109, 111, 121
Angular momentum operator, 111, 112, 144, 151, 157
Anharmonicity, 170
Anomalous Zeeman effect, 103, 105
Antibodies, 62
Antimalaria agents, 39
Antisymmetric operator, 111
Antisymmetry, 111
Antitumor agent, 38
Aqueous diffusion, 228
Aqueous solution, 205
Associated rate constants, 206
Association rates, 63
Association rates of proteins, 75
Asynchronous movement, 213
Atomic hydrophobicity constants, 26
Atomic solvation parameters (ASP), 28, 70, 71, 81
Atoms, 172
Aufbau principle, 108
AutoDOCK
, 2, 16
Automated docking, 41, 43
Automated protein-protein docking, 69
Automation, 61
Available Chemicals Directory (ACD)
, 30, 38, 39
Avoided crossing, 177, 178

Backbone flexibility, 81, 85, 87, 88
Backtracking, 14
Barnase, 63, 64, 65, 66, 82, 83, 84, 89
Barstar, 63, 64, 65, 66, 82, 89
Base fragments, 12
Basis set expansion, 191
Basis states, 101
Bayesian regression, 29
Belousov-Zhabotinsky oscillating reaction, 242
Benchmark docking, 91
Bezier splines, 18
Biased distortions, 81
Binding affinity, 2, 3, 11, 23, 24, 29, 33, 34, 38, 42, 63
Binding conformations, 67
Binding data, 62
Binding free energies, 3, 23, 26, 27, 30
Binding mode, 2, 25, 40, 44, 82
Binding site, 2, 31, 36, 44
Bioinformatics, v, 61
Biological screening, 37
Biotechnology, 62
Biotin, 30, 39
Bit string, 14
BLEEP function, 33
BLEEP1, 32
BLEEP2, 32
Blind prediction, 41
BNSOC
, 169
Bohr-Sommerfeld theory, 121
Boiling point, 223
Boltzmann distribution, 179
Born equation, 27
Born-Oppenheimer effects, 161
Boson irreducible representations, 140, 158
Bound electronic states, 187
Bound-bound interactions, 188
Bound-continuum interactions, 189
Boundary cell, 210
Bra-ket notation, 128
Branch & bound, 20
Breaking parameters, 226
Breaking probability, 216, 223
Breaking rules, 216
Breit-Pauli spin-orbit Hamiltonian, 125, 193
Breit-Pauli spin-orbit integrals, 161
Breit-Pauli spin-spin coupling operator, 147
Breit-Pauli theory, 182
Brownian dynamics, 75, 84
BUILDER
, 23
Bulk solvent, 81
Buried surfaces, 31, 34, 78

CAChe
, ix
Calmodulin, 79
Cambridge Structural Database (CSD)
, 14, 39
CAMLab
, 19
Carbon monoxide, 189
Cartesian coordinates, 18
Cartesian Gaussians, 161
Cartesian space, 17
Cartesian triplet spin functions, 180
Cathepsin D, 23
Cell, 209
Cell membrane, 232
Cell movement, 212
Cell shape, 210
Cellular automata, xi, 205, 207, 208
CH radical, 175
Character table, 141, 142
Charge complementarity, 65
CHARMM
, 27, 64
CHARMm force field, 19
CHARMM force field, 82
Chemical Abstracts
(CA) database, v
Chemical Abstracts Service (CAS), v
Chemical complementary scores, 25
Chemical matching, 25
Chemical properties, 205
Chemical reactions, 205
Chemical scores, 24, 25
Cheminformatics, v
ChemScore
, 34
Chromatographic separation, 216, 247
Chromosome, 15
CIPSO
, 170
Clebsch-Gordan (CG) coefficient, 149
Clique-detection algorithm, 7
Clique-search, 6, 18
CLIX
, 7
Cluster, 9
Clustering, 10, 22
Cocrystallized ligands, 30
Cocrystallized protein structures, 41
COLUMBUS
, 169
CombiDOCK
, 22
Combinatorial chemistry, 21, 37, 40
Combinatorial docking, 22
Combinatorial libraries, 21
Combinatorial optimization, 3, 16, 81
Commutation relations, 113, 115
Compatibility, 6
Complete enumeration, 75
Complete-linkage hierarchical clustering, 10
Complexity, 221
Compound acquisition, 37
Compound tensor operators, 145
Computational docking studies, 67
Computer-aided ligand design, x
Concoord method, 83
CONCORD
, 36
Configuration, 220
Configuration interaction (CI), 127, 149, 160, 163
Configuration state functions (CSFs), 166
Conformational change, 24, 83
Conformational ensemble, 11, 83
Conformational entropy, 29
Conformational flexibility, 70, 82
Conformational search techniques, 79
Conformational space, 2, 11, 74
Conformations, 13, 14, 18, 19, 21
Consensus scoring, x, 4, 33, 44
Conserved binding site, 42
Contact scores, 24
Containment potentials, 27
Continuum wave functions, 189
Contracted basis sets, 162
Cooling schedule, 16
Copper atom, 173
Core molecule, 22
Core-electron integrals, 129
Core-valence integrals, 129
CORINA
, 14, 36
Correlation energies, 169
Correspondence principle, 121
Coulomb integral, 129, 131, 161
Coupled differential rate equations, 206
Coupled-cluster electronic structure, 166
Coupling procedures, 167
Critical Assessment of Structure Prediction (CASP), 41, 91
Critical Assessment of Techniques for Free Energy Evaluation (CATFEE), 41, 91
Critical lipophilicity, 233
Critical micelle concentration, 232
Critical state of association, 235
Cross-docking experiments, 41
Crossing point, 190
Crystal disruption, 226
Curve crossings, 187, 191
Cyclin, 67, 68
Cyclin-dependent kinase 2, 67, 68
Cytochrome, 82

Darwin corrections, 159
Databases, v, 3, 82
Davidson method, 168
db_translate
, 36
De novo ligand design, 2, 4, 11, 22, 23, 28, 31
Dead-end elimination (DEE), 20
Decoy complexes, 91
Degenerate states, 171
DelPhi
, 42, 77
Demixing of immiscible liquids, 216
Derivatives, 161
Desolvation, 27
Desolvation energies, 70, 88
Deterministic cellular automata, 213
Deterministic rules, 209
Dielectric constant, 26, 27, 28, 72, 77, 224
Diffusion, 224, 228, 232
Digital computers, 209
Dihedral angle space, 86
Dihydrofolate reductase (DHFR), 25, 39
DING HAO
, 249
Dipolar spin-spin coupling operators, 147
Dipole moments, 182
Dirac theory, 107, 109, 124, 125
Dirac-Coulomb-Breit operator, 124
Direct methods, 168
Discontinuous microscopic events, 206
Discrete water molecules, 14
Disorder-order transition, 67
Dissociation constants, 63
Dissociation energy, 187
Dissociation rates, 63
Dissociative electronic state, 190
Dissolution, 226
Distance compatibility, 6, 18
Distance geometry methods, 11, 18
Distance matrix, 18
Distribution, 38
Dithiosuccinimide, 183
DNA dodecamer-netropsin complex, 39
DOCK
, 2, 4, 6, 7, 19, 25, 26, 32, 33, 34, 35, 38, 43, 78
Docked conformations, 26
Docking, x, 1, 37, 61, 69, 70, 90
Docking programs, 29
DOT
, 77
Double excitations, 128, 129, 130
Double groups, 140, 143, 158, 194
DREAM++
, 23
Dressed Hamiltonians, 195
Drug, 45
Drug design, 21, 62
Drug discovery, 1, 37, 45, 221
Drug-like molecules, 3, 10, 11, 38, 39, 44
Drug-receptor encounters, 221
Drug-score, 33
Dynamic correlation effects, 195
Dynamic properties, 66

ECEPP/3 force field, 18
Effective core potentials (ECP), 136, 193, 194
Effective one-electron spin-orbit Hamiltonians, 132
Effective potential, 162
Eigenvalues, 116
Eigenvectors, 118
Electric dipole, 186
Electric dipole transitions, 105, 181
Electron correlation, 127, 159, 167
Electron spin, 101, 103, 108
Electron spin resonance (ESR), 100
Electronic spin-spin coupling, 147
Electronic states, 126, 170
Electrostatic calculations, 42
Electrostatic complementarity, 26
Electrostatic continuum, 26
Electrostatic energies, 170
Electrostatic interactions, 65, 72
Electrostatic solvation, 18
Electrostriction, 224
Emergent properties, 221
Empirical atomic hydrophobicities, 25, 26
Empirical one-electron operators, 132
Empirical scoring functions, 24, 28, 29, 34
Empiricism, 206
Encounter complexes, 88
Energy score, 33, 34, 43
Enrichment, 5, 40
Ensemble enriching multiple copy molecular dynamics, 90
Ensembles, 21
Enthalpy, 71
Enthalpy-entropy compensation, 65
Entropy, 24, 26, 81
Entropy changes, 24
Entropy terms, 27
Enzyme reactions, 245
Enzymes, 245
EPCISO
(Effective and polarized spin-orbit CI), 170
EPDOCK
, 15
Epitope, 64
Epstein-Nesbet perturbation theory, 169
Equilibrium, 244
Equilibrium constant, 238
Error rates in CA databases, vi
Essential dynamics, 83
Estrogen receptor, 39
Ethene, 135
Euclidean space, 18
Euler angles, 137
Euler rotation matrix, 140
Evolution, 14
Evolutionary programming, 14
Exchange integrals, 129
Excitations, 183
Excited state, 177, 241
Excited-state kinetics, 240
Excited-state lifetimes, 242
Exclusion principle, 108
Excretion, 38
Extended von Neumann neighborhood, 213

Factor Xa, 39, 41
False negatives, 4, 38
False positives, 3, 34, 38, 44, 77
Farnesyltransferase inhibitors, 39
Fast Fourier transforms, 76
Fermion irreducible representations, 140, 158
Filter functions, 34
Fine-structure splitting, 99, 134, 159, 170, 173, 193, 194
Finite basis, 162
First-order kinetics, 237
First-order perturbation theory, 126
First-order spin-orbit perturbation, 180
First-order spin-orbit splitting, 171
First-order transitions, 240
First-rank tensor operator, 144
Fitness function, 14, 15
Fitness score, 88
FK506-binding protein, 25, 32, 34, 39
FlexE
, 21
Flexibase/FLOG docking algorithm, 11
Flexibases, 11
Flexibility, 83, 88
Flexibility penalty term, 29
Flexible docking, 10, 33, 39, 70, 74, 79, 80, 86, 88
Flexible ligands, x, 2, 11
FlexX
, 2, 13, 19, 28, 32, 33, 35, 39, 40
FlexX
, 23
FLOG
, 2, 27, 34, 39
Flowchart of docking, 35
Fluctuations, 208, 238, 244
Fluorescence, 183, 192, 241
Fold prediction, 62
Foldy-Wouthuysen transformation, 126
Force field, 19, 26, 28, 34, 207
Force field scoring, 26
Four-component ab initio method, 159
Fragment-based de novo ligand design, 23
Fragmentation, 11
Franck-Condon (FC) factors, 188
Free energies, 26
Free energy of binding, 28, 70, 83, 86
Free energy perturbation, 24, 70
Free movement probability, 215
Frozen-core approximation, 127
Frozen-core orbitals, 127
Frozen-core spin-orbit Hamiltonian, 129
FTDOCK
, 77, 83, 85, 87
Full CI, 165
Fuzzy logic, vi

GAMBLER
, 34
Gaussian basis functions, 162
Gaussian lobe functions, 161
General angular momenta, 114
Generalized Born/surface area, 27
Genetic algorithms (GA), 14, 88
Genetic docking algorithm, 40
Genomes, 62, 90
Geometric features, 8
Geometric hashing, 7, 8, 12, 78, 79, 80
Global energy minima, 20, 25
Global optimum, 5
GOLD
, 2, 15, 27, 35, 40
Gordon Research Conferences (GRCs), ix
Gradient-based techniques, 74, 81
GRAMM
, 77
Graph theory, 6
Gravity effect, 210, 216, 229
GREEN
, 26
Grid, 16, 17, 26, 75
Ground state, 102
GROW
, 13

Haloperidol, 39
Hamiltonian: Breit-Pauli spin-orbit, 125, 193
Hamiltonian: Dressed, 195
Hamiltonian: Effective one-electron spin-orbit, 132
Hamiltonian: Frozen-core spin-orbit, 129
Hamiltonian: Magnetic interaction, 146
Hamiltonian: Mean-field, 135
Hamiltonian: No-pair spin-orbit
Hamiltonian: No-pair, 126, 167
Hamiltonian: Phenomenological spin-orbit, 147, 194
Hamiltonian: Spin-orbit, 124
Hamiltonian: Valence-only spin-orbit, 127
Hamiltonian: Zeroth-order regular approximation (ZORA), 167
Hamiltonians, 100, 111, 124, 125, 127, 130, 132, 135, 143, 146, 151, 158, 159, 171, 175, 193
Hammerhead
, 2, 14, 29
Haptic devices, 69
Hash table, 8, 12
Hashing, 7, 78, 79
Hashing function, 8
Hashing key, 8
Heat capacity, 224
Heavy atoms, 133, 174
Heavy elements, 100
Helicopter view, 17
Hemagglutinin, 38
Hermite Gaussian functions, 161
Hermitian, 111
Heuristic rules, 208, 248
Heuristic scoring schemes, 24
Hidden bias, 40
High throughput screening (HTS) methods, 4, 37
Hinge, 12
Hinge-bending motion, 67, 79
HINT
, 25
HIV reverse transcriptase, 39
HIV-1 protease inhibitor, 39
Hole states, 172
Homology models, 2, 62, 90
Hot spot residue, 86
Hot spots, 63
Human growth hormone, 64
Human immunodeficiency virus (HIV-1) protease, 4, 8, 25, 30, 31, 38, 39
Hund's case, 171, 174, 175
Hybrid methods, 19
Hydration, 82, 224
Hydration energy, 27
Hydrides, 171
Hydrogen bond potentials, 27
Hydrogen bonding, 13, 15, 26, 27, 28, 64, 86
Hydrophobic effect, 224
Hydrophobic interactions, 32, 65
Hydrophobic potentials, 27
Hylleras perturbation theory, 166
HyperChem
, ix
Hyperfine splittings, 100, 146

Identity, 101, 141
Immiscible liquids, 229, 231
Implicit solvation model, 91
Incremental construction, 11, 13, 19, 22
Induced fit, 75, 82
Infinitesimal rotation, 109
Infinitesimal rotation operator, 112
Influenza virus, 41
Influenza virus neuraminidase, 2
Informatics, v
Inhibitors, 62
Inosine monophosphate dehydrogenase, 4
Integrals, 131
Intensity borrowing, 182
Interaction center, 10
Interaction energy, 24
Interaction surface, 10
Interface surface patches, 62
Interfacial side chains, 79, 81
Interfacial surfaces in proteins, 62, 63, 83
Interleukin-4-alpha receptor, 64
Internal conversion (IC), 178, 241
Internal Coordinate Mechanics (ICM)
, 17, 18
Internal coordinate mechanics, 81
Internal coordinates, 17
Intersystem crossings (ISC), 100, 161, 178, 186, 193, 241
Intraligand interactions, 27, 32
Inverted state, 172
Ion-pair interactions, 28
Ionic solvation effects, 235
Ionic strength, 65
Irreducible representation, 136, 140
Irreducible tensor operators, 148

Jablonski diagram, 178
jj coupling, 167
Joining parameters, 226
Joining trajectory parameter, 216
Journal of Chemical Information and Computer Science
, xii
Journal of Computational Chemistry
, xii
Journal of Computer-Aided Molecular Design
, xii
Journal of Molecular Graphics and Modelling
, xii

Kinetic behavior, 206
Kinetic reaction control, 240
Kirkwood equation, 81
Knowledge-based potentials, 30
Knowledge-based scoring functions, 24, 30
Kohn-Sham approximation, 167
Kramers degeneracy, 168
Kramers pairs, 167
Kronecker delta, 113

Ladder operators, 114
Laguerre polynomials, 78
Landé interval rule, 133, 172, 173, 174
Langevin dipoles, 81
Large-scale conformational changes, 67, 79, 83
Lead identification, 37, 43
Lead optimization, 2, 40, 41, 43
Lead structures, 5
Lennard-Jones function, 27, 72
Library design, 38
Lifetime calculations, 186
Lifetime of an excited state, 179
Ligand database, 36
Ligand design, 2, 40, 45
Ligand fragments, 41
Ligand solvation, 27
Ligand-binding site, 5
LIGIN
, 19
LIGSITE
, 36
Limited backtrack search, 14
Linear molecules, 156, 174
Linear momentum operator, 129
Linear representation, 14
Linear response approximation, 24
Lineweaver-Burk plots, 245
Lipophilic fragments, 231
Lipophilic interactions, 28
Lipophilicity, 29, 229, 245
Local minima, 17, 19
Local structural changes, 66
Long-range electrostatic interactions, 88
LS contracted spin-orbit configuration interaction, 165
LUDI, 7, 9, 10, 23, 28
Luminescence quantum yields, 242
Lysozyme, 63
Lysozyme-Hyhel5 antibody complex, 81

Macroscopic phenomena, 206
Magnetic dipole transition operator, 186
Magnetic dipole transitions, 182, 186
Magnetic dipoles, 102, 186
Magnetic field, 101, 103, 108
Magnetic interaction Hamiltonians, 146
Magnetic interactions, 99, 100
Magnetic quantum numbers, 107
Magnetic resonance, 159
Malaria protease, 38
Manual docking, 41
Markov chain, 19
Markov processes, 206
Mass spectrometry (MS), 62
Mass-velocity corrections, 159
Matrix elements, 148
Matrix elements of angular momentum operators, 119
Matrix metalloproteinase stromelysin (MMP-3), 33
MCM method, 18
MCSS technique, 23
MDL databases, 36
Mean-field approximation, 185
Mean-field Hamiltonian, 135
Mean-field potentials, 33
Mean-field scoring function, 31
Mean-field spin-orbit operators, 162
Melting process, 226
Membrane, 231, 232
Membrane permeability, 232
Metabolism, 38
Metallo-beta-lactamase inhibitors, 39
Methylene, 155, 156
Metropolis criterion, 16, 81
Micelle formation, 231
Michaelis-Menten model, 245
Microcalorimetry, 23
MIMUMBA (torsional angle database), 36
Misspellings, vii
Mitogen-activated protein (MAP) kinase, 4
Molecular affinity potentials, 16
Molecular docking, 4, 7
Molecular dynamics, 4, 16, 70, 82, 207
Molecular fragments, 4
Molecular mechanics, 71, 75
Molecular recognition, 1, 16
Molecular simulation, 16
Molecular Simulations, Inc., viii
Molecular structures, 208
Molecule fragments, 6
Momentum operator, 194
Monte Carlo (MC) algorithms, 17, 19
Monte Carlo simulations, 206, 207
Monte Carlo trajectories, 82
Moore neighborhood, 213
Movement probability, 215
Movement rules, 213, 215
Moving cell, 210
Multiconfiguration self-consistent field (MCSCF), 166, 169
MULTIDOCK
, 79
Multiple copy MD, 89
Multipole expansion, 186
Multireference CI, 183
Multireference CI wave functions, 185
Multireference singles and doubles CI (MRSCDI), 169

Natural orbitals (NOs), 169
Neighborhoods, 212, 213
Neuraminidase, 32, 34, 41
Neuraminidase inhibitors, 42
Newtonian mechanics, 16
Nickel atom, 173, 174
Nitric oxide, 179
No-pair Hamiltonian, 167
No-pair operators, 162
No-pair spin-orbit Hamiltonian, 126
Non-rotameric states, 81
Nonbonded cutoff schemes, 28
Nonlinear molecules, 154
Nonoccluded atom pair interactions, 29
Nonradiative depletion mechanisms, 183, 186
Nonradiative processes, 241
Nonradiative transitions, 100, 161, 177, 187, 192, 193
Normal mode analysis, 83
Normal Zeeman effect, 103
Nuclear magnetic resonance (NMR), 1, 39, 62, 100
Nuclear Zeeman effect, 107

Obituaries, vii
One-electron integral, 128
Onset of percolation, 236
Open-shell electronic states, 133
Operator: Angular momentum, 111, 112, 144, 151, 157
Operator: Antisymmetric, 111
Operator: Breit-Pauli spin-spin coupling, 147
Operator: Compound tensor, 145
Operator: Dipolar spin-spin coupling, 147, 147
Operator: Dirac-Coulomb-Breit, 124
Operator: Empirical one-electron, 132
Operator: First-rank tensor, 144
Operator: Infinitesimal rotation, 112
Operator: Irreducible tensor, 148
Operator: Ladder, 114
Operator: Linear momentum, 129
Operator: Magnetic dipole transition, 186
Operator: Matrix elements of angular momentum, 119
Operator: Mean-field spin-orbit, 162
Operator: Momentum, 194
Operator: No-pair, 162
Operator: Phenomenological electronic spin-spin, 176
Operator: Phenomenological, 152
Operator: Projection, 101
Operator: Pseudo-potential spin-orbit, 133
Operator: Relativistic kinetic energy, 127
Operator: Scalar, 144
Operator: Second-rank tensor, 144
Operator: Shift, 114, 171
Operator: Spin, 122
Operator: Spin-orbit coupling, 133
Operator: Spin-orbit mean-field, 134
Operator: Spin-orbit, 125, 147
Operator: Step, 144
Operator: Step-down, 114
Operator: Step-up, 114
Operator: Step/shift/ladder, 114
Operator: Symmetry, 143
Operator: Tensor, 137, 143, 145, 146, 171
Operator: Vector, 144
Operator: Wood-Boring spin-orbit, 134
Optimal rigid-body orientation, 75
Optimization, 16, 88
Orbital angular momentum, 109, 112
Oscillator strengths, 182
Osmotic effect, 233
Oxygen, 100, 179, 187, 190, 192, 242

Parallel Virtual Machine (PVM)
, 37
Partial protein flexibility, 21
Particle concept, 14
Particle states, 172
Partitioning, 229
Paschen-Back effect, 106, 108
Passive diffusion, 232
Pattern recognition, 9
Pauli principle, 99, 108
Pauli spin matrices, 123
Percolation, 235
Percolation threshold, 236
Perturbation expansion theory, 181
Perturbation theory, 186
Perturbational approaches, 163
pH, 65
Pharmacophore, 26
Phase changes, 205
Phenomenological electronic spin-spin operator, 176
Phenomenological operators, 152
Phenomenological spin-orbit Hamiltonian, 147, 194
Phospholipase A2, 2
Phosphorescence, 100, 179, 183, 193, 241
Phosphorescence lifetimes, 186
Physical properties, 205
Pi-stacking interactions, 28
Piecewise linear potential (PLP), 25, 34
Place & join, 11
Placement lists, 12
Planck's constant, 102
Plastocyanin, 82
PLP scoring function, 25
PMF-score, 33, 34, 43
Poisson equation, 19
Poisson-Boltzmann electrostatic forces, 75, 81, 82
Poisson-Boltzmann equation, 18, 72, 77
Pose clustering, 9, 13
Positronic states, 126
Postprocessing, 37
Potential energies, 26, 101
Potential energy curves, 188
Potentials of mean force (PMF), 30
Predissociation, 187, 190, 191, 194
Preequilibrium, 240
PRO_LEADS
, 19, 29
PRO_SELECT
, 22
Probabilistic cellular automata, 214
Probabilistic microscopic events, 206
Probabilistic movement rules, 213
Probabilistic rules, 209
Probability amplitudes, 101
PRODOCK
, 18
Profit, 45
Projection operators, 101
Proprietary databases, 37
Proteases, 62
Protein complexes, 69
Protein Data Bank (PDB)
, 1, 31, 32, 73
Protein engineering, 63
Protein flexibility, 5, 20, 21, 44, 79
Protein folding, 30
Protein structure evaluation, 30
Protein structures, 2, 26
Protein surfaces, 62
Protein targets, 1
Protein binding pocket, 24
Protein-ligand binding, 20, 28, 29
Protein-ligand binding affinities, 31
Protein-ligand complex, 1, 2, 19, 24, 28, 30, 40, 44, 45
Protein-ligand conformations, 27, 34
Protein-ligand docking, 5, 16
Protein-ligand interactions, 25, 30, 36
Protein-ligand interface, 14
Protein-ligand scoring functions, 30
Protein-protein binding, 65
Protein-protein docking, 61
Protein-protein interactions, 28
Protein-protein interfaces, 62, 67, 70, 87
Proteins, 30
Proteomics, x, 90
Protonation states, 36
Pseudo-first-order reaction, 245
Pseudo-potential spin-orbit operators, 133

Quadratic shape descriptors (QSD), 26
Quantum chemistry, 99
Quantum effect, 108
Quantum field theory, 107
Quantum mechanics, xii, 101
Quantum numbers, 108, 148, 150, 193
Quantum Theory Project (QTP), ix
Quasi-degenerate perturbation theory, 133, 165, 168, 186
QXP
, 17

R-group selection, 23
Radial amplitudes, 160
Radiation field, 186
Radiative depletion, 187
Radiative lifetimes, 185, 187
Radiative processes, 240
Radiative transitions, 179, 193
Radioactive decay, 237
Random search, 19
Rate constants, 206
Rate-limiting-step, 240
Rational drug design, 45, 62
Rayleigh-Schrödinger perturbation theory, 163, 179
Reaction-diffusion systems, 242
Receptor critical points, 78
Receptor site, 5, 11, 13, 17, 19, 36, 41
Reduced matrix element, 151
Reference frame, 8
REGISTRY database
, v
Regular state, 172
Regulating membrane passage, 233
Relative gravity parameter, 219
Relativistic CI (RCI), 169
Relativistic corrections, 159
Relativistic effect, xi, 99, 194
Relativistic effective core potentials (RECP), 133, 159
Relativistic effective pseudo-potentials, 134
Relativistic field theory, 124
Relativistic kinetic energy operator, 127
Relativistic quantum theory, 101
Reorganization energy, 24
Response theory, 166, 179
Retardation term, 125
Reversible second-order reaction, 244
Reviews in Computational Chemistry
, vi, xii
Rigid docking, 26, 39
Rigid molecules, 6
Rigid-body docking, 6, 11, 19, 69, 73, 74, 81, 83
RNase H, 38
Rotamer library, 81
Rotatable bonds, 11, 28
Rotation matrices, 138
Rotational angle space, 77
Rotational predissociation, 192
Rovibronic coupling, 161
Rovibronic spectra, 170, 171, 187
Rule-based format translation, 36
Russell-Saunders (LS) coupling, 155, 156
Russell-Saunders states, 182
Rys quadrature techniques, 161

Salt bridges, 26, 86
Sampling, 3, 70
Sampling properties, 19
SANDOCK
, 26
Sanibel Symposia, ix
SAR by NMR, 41
Scalar operator, 144
Schrödinger equation, 113, 187, 188
Schumann-Runge bands, 190
SciFinder
, v, vi
SCORE
, 34
Scoring, 1, 23, 33, 70, 71, 77
Scoring functions, x, 3, 15, 19, 24, 44, 69, 75
Screening methods, 1
Second-order kinetics, 242
Second-order rate law, 243
Second-order spin-orbit splitting, 175
Second-rank tensor operator, 144
Selection rules, 137, 146, 158
Self-quenching rates, 177
Self-reproducing automata, 208
Semiempirical molecular orbital method, viii
Shannon information content, 237
Shape complementary scores, 24, 25, 26
Shift operators, 114, 171
Sialic acid, 42
Side-chain conformations, 20, 36, 66, 67, 73, 81, 86, 87
Side-chain flexibility, 86
Side-chain optimization, 81, 86
Side-chain torsion dynamics, 88
Silver atoms, 101
Simian immunodeficiency virus (SIV), 30
Simulated annealing, 16, 75
Single excitations, 128, 129, 130
Size extensive, 165
Skew symmetric matrix, 168
Slater determinants, 128
Slater-Condon rules, 129, 163
Slater-type orbitals (STOs), 161
Small fragments, 41
SMoG
, 31
Soft van der Waals potentials, 27, 28
Solubility, 224
Solute dissolution, 226
Solution phenomena, 210
Solvated interfacial region, 86
Solvation, 18, 91
Solvation energies, 24, 25, 27
Solvation free energy, 28, 81
Solvent effects, 183
Solvent-accessible surface (SAS), 18, 20, 26, 32, 65, 71, 82
SPDIAG
, 169
SPECITOPE
, 21, 26
Spherical harmonics, 78, 112
Spin, 99, 101, 108, 121, 159
Spin angular momentum, 108, 121
Spin density functional methods, 167
Spin flip, 186
Spin magnetic moment, 108
Spin multiplet, 99
Spin orbitals, 128
Spin-coupling coefficients, 150
Spin-forbidden electric dipole transition, 194
Spin-forbidden radiative transitions, 179, 182
Spin-forbidden transitions, 100, 177, 186
Spin-free frozen-core approximation, 127
Spin-free state shifted (SFSS) SOCI method, 169
Spin operators, 122
Spin-orbit CI, 168, 179, 194
Spin-orbit coupling, xi, 99, 146, 152, 156, 159, 163, 167, 168, 177, 193
Spin-orbit coupling operators, 133
Spin-orbit Hamiltonians, 124
Spin-orbit integrals, 161
Spin-orbit mean-field operator, 134
Spin-orbit operators, 125, 147
Spin-orbit perturbed wave functions, 179
Spin-orbit splitting, 157, 194
Spin-polarization, 160
Spin-spin coupling, 100, 124, 147, 156
Spin-spin interaction, 194
Spin-vibronic interactions, 185
Spinor transformations, 139
Spinors, 122, 136
Steady-state approximation, 240
Step operators, 144
Step-down operators, 114
Step-up operators, 114
Step/shift/ladder operators, 114
Stern-Gerlach experiment, 100, 101, 102
Stern-Volmer plot, 177
STN
system, v
Stochastic dynamics, 75
Stochastic master equation, 206
Strain energy, 26, 34
Streptavidin, 30, 39
Stromelysin, 32
Structurally diverse compounds, 3
Structure-activity relationships (SAR), 2
Structure-based ligand design, 40
Sum-over-states methods, 166, 194
Supermultiplet approach, 170
Surface charges, 28
Surface complementarity, 25, 29, 31, 34
Surface features, 78
Surface descriptors, 25
Surface matching algorithm, 17
Surface plasmon resonance, 23
Surface-related properties, 29
SYBYL
, 34
Symmetry, 136, 165
Symmetry operators, 143
Synchronous movement, 213
Synthesis, 3

Tabu list, 19
Tabu search, 19
Taylor series, 138
Template molecule, 22
Tensor operators, 137, 143, 145, 146, 171
Tensor properties, 146
Thallium atom, 160
Theoretical Chemistry Accounts
, xii
Thermodynamic reaction control, 240
Thiocarbonyls, 183
Thrombin, 39
Thrombin inhibitors, 23, 33
Thymidylate synthase, 38
Time-dependent perturbation theory, 187
Time-dependent populations, 206
Torsion dynamics, 86
Torus, 210
Toxicity, 38
Transition functions, 213, 215
Transition moment, 181, 182
Transition probabilities, 159, 178, 182
Transition rate, 208
Transition rules, 215
Tree structure, 22
True hit, 38
True positives, 38
Truncated CI expansion, 165
Trypanothione reductase, 39
Two-electron integrals, 135

UHBD
, 77

Valence electron, 107
Valence-only spin-orbit Hamiltonian, 127
VALIDATE
, 29
van der Waals interactions, 72
van der Waals potential, 18, 26, 27, 28
Vapor pressure, 224
Variational collapse, 167
Variational perturbation theory, 166, 179, 194
Variational procedures, 166
Variegated cell, 211, 231
Vector operator, 144
Vibrational averaging, 174
Vibrational continuum, 187
Vibrational coordinate, 170, 188, 191
Vibrational wave functions, 188, 190, 194
Vibrationally bound states, 188
Vibrationally unbound states, 194
Viral replication cycle, 42
Virtual compounds, 3, 38
Virtual photons, 124
Virtual reality, 69
Virtual SAR by NMR, 4
Virtual screening, 3, 4, 13, 21, 35, 37, 43, 44
Viscosity, 224
Volume overlap, 25
von Neumann neighborhood, 213, 222

Water, 9, 32, 63, 65, 81, 86, 91, 210, 213, 221, 224
Water clusters, 224
Water properties, 226
Water structure, 235
Water-mediated hydrogen-bonding, 86
Wave functions: Continuum, 189
Wave functions: Multireference CI, 185
Wave functions: Spin-orbit perturbed, 179
Wave functions: Vibrational, 188, 190, 194
Weakly active chemical entities, 34
Wentzel-Rice formula, 189
WHAT IF
, 64
Wigner-Eckart theorem, 137, 148, 156, 158, 193
Wood-Boring spin-orbit operators, 134
Workstation clusters, 37
World Drug Index
, 39

X-PLOT
, 64
X-ray crystallography, 1, 62

Zeeman effect, 103, 105
Zeeman spectroscopy, 100
Zero-field splitting, 99, 193
Zeroth-order regular approximation Hamiltonian (ZORA), 167
ZINDO
, viii

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