REVIEWS IN COMPUTATIONAL CHEMISTRY

Subject Index, Volume 7 (1995)

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 theory, 245
ABACUS
, 362
AbM
, 367
Accessible surface areas, 91
Accord
, 324
ACeDB
, 326
ACES II
, 356
Acetic acid, 141
Acetone, 165, 166, 167
Acetonitrile, 166
Acetylcholinesterase, 168
Acetylene, 168, 236
Acrolein, 241
ACS Directory of Graduate Research
, 322
ACS Software, 332
Active analog approach, 86
ADAPT
, 374
Adenine, 147, 148, 149, 251, 252
ADF
, 229, 357
Advanced Visual Systems, Inc., 370
Agglomerative clustering, 26, 28
Agrochemical Patent Fast Alert
, 370
AGRO-METABOLEXPERT
, 344
AI Ware, 338
AIMPAC
, 357
Air Toxics database
, 332
ALADDIN
, 53, 86
Alanine dipeptide, 247, 248, 249, 250
Alchemy II
, 361
Alchemy III
, 317
Alcohols, 291
Aldrich Catalog
, 324
Alignment, 14, 55
Alignment rules, 95
Allenes, 291
Allyl vinyl ether, 155, 157
Alpha-amylase, 107
Alpha-chymotrypsin, 46
Alpha-pinene, 264
Alvis
, 378
AM1, 121, 135, 138, 139, 140, 143, 156, 166, 168, 299, 357
AM1-SCRF, 153
AM1-SM2, 147, 153, 155
AM1/TIP3P simulations, 156, 161
AM2000
, 348
AMBER
, 139, 147, 308, 314, 348, 349, 367
American Chemical Society (ACS), 306, 308, 332
American Crystallographic Association (ACA), 308
American InterFace Computer, Inc., 374
American Molecular Technologies, Inc., 348
Amide isomerization, 152
Amides, 152
Amorphous Cell
, 351
AMPAC
, 324
AMSOL
, 362
Anaconda
, 367
Analysis
, 351
Analytic energy gradients, 230
Analytical Chemistry by Opening Learning
, 332
Andataco Computer Peripherals, 372
Angiotensin II antagonists, 88, 90, 93, 109
Angular information, 35
Animated Demonstrations II
, 341
ANNEAL-RING
, 348
Antheprot
, 367
Antibody-antigen interface, 48
Antihistamine pharmacophore, 82
Apex-3D
, 351
Apple Computer, 308
APSO
, 378
Aptech Systems, Inc., 341
Ar, 166
Archie, 306
ARGOS
, 321
ARGUS
, 139, 357
ARPAnet, 306
ARSoftware, 345
Art of Science
, 338
ARTHUR
, 335
ARVOMOL
, 324
Asp
, 367
Association coefficient, 20
ASTERIX
, 358
Asymmetric coefficient, 29
Atlantic Software, 331
ATLAS of Protein and Genomic Sequences
, 325
Atmospheric Oxidation Rate Program
, 334
ATOM
, 322
Atom environment, 74
Atom pair fragment, 8
Atom triangles, 105
Atom triplet, 35, 105
Atom typing, 72
Atom-based superimposition, 55
Atom-by-atom search, 7, 11, 15, 24
ATOMCI
, 361
Atomic axial tensor, 270
Atomic charges, 150
Atomic polar tensor model, 266, 270
Atomic polarizability, 125
Atom-mapping, 33, 39, 45
Atom-match matrix, 39
Atom-pair structural fragments, 22
ATOMPLUS
, 323
ATOMSCF
, 361
AUTODOCK
, 47, 348
AUTONOM
, 321
Auxin transport, 87
Available Chemicals Directory
, 369
Average distance sum connectivity index, 16
Average solvent effects, 149
AVS
, 370
AVS ChemistryViewer
, 354
Azabicyclohexane, 287, 288
Aziridines, 285

Babel
, 332
BAKMDL
, 352
Balaban index, 16
Ball & Stick
, 330
Basic nitrogen, 72
Basis functions, 209, 226
Basis set superposition, 210
Basis set 3-21G, 161, 168, 277, 278
Basis set 3-21G*, 243
Basis set 3-21G**, 243
Basis set 4-31G, 168
Basis set 6-31G~, 274, 279, 292
Basis set 6-31G(d), 141, 142, 143, 156, 162, 165, 236
Basis set 6-31G(ext), 277
Basis set 6-31G(pol), 277
Basis set 6-31G*, 248, 250, 252, 253, 273, 274, 276, 278, 279, 280, 286, 293
Basis set 6-31G*(0.3), 276, 280, 281, 286, 294
Basis set 6-31G**, 278, 281, 290, 292
Basis set 6-31+G**, 250
Basis set 6-311++G(2d,2p), 246
Basis set Double zeta plus polarization, 252, 253
Basis set pVTZ(++), 276
Basis set STO-3G, 168
Basis set Triple zeta plus polarization, 248, 250
Basis set vd/3p, 276, 279, 280
Basis-set-free calculations, 210
BBN Systems and Technologies Corporation, 353
Beilstein Handbook database
, 318, 325, 329
Beilstein Information Systems, Inc., 326
Bemis-Kuntz algorithm, 34
BENDER
, 369
Benzene, 167
BEST North America Database
, 337
BESTFIT
, 377
Biblio-Link II
, 346
Biblio-Links
, 346
BibTex
, 347
BIGSTRN3
, 362
Bin distribution, 78
BioByte Corp., 374
Biobyte Medchem Masterfile
, 366
BioCatalysis
, 324
Biochemistry
, 332
BIODEG
, 334
Biodegradation Probability Program
, 334
BIOEQ/PHSEQ
, 374
BIOGRAF
, 354
BIOLOG
, 334
Biomolecular modeling, 217, 233
Biomos B.V., 350
Bionet, 308
Biopolymer
, 351
BIOPROP
, 337
Biosoft, 335
BioSoftware Marketing, 333
BioSPECS database
, 366
BIOSTAR
, 370
BIOSYM Technologies, Inc., 308, 314, 350, 359
Biotechnology Citation Index
, 339
BioWorld Online
, 337
Birkbeck College, 308
Bitnet, 306
Bit-string, 9, 45
BLDKIT
, 369
BLOGP
, 318
BLOGW
, 318
BLSS
, 337
B-LYP approach, 234, 235
BNDPKG2
, 361
Boltzmann weighting, 292
Bond breaking and formation, 123
Bond dipole model, 266
Bond energies, 236
Bond-centered fragments, 8
Bookends Pro
, 337
Born-Oppenheimer approximation, 188, 233, 247, 263
BOSS
, 139, 355, 367
Boundary conditions, 123, 127
Boundary force, 128
Bounded distance matrix, 45
Bounds smoothing, 11
Br2, 166
BrainMaker Professional
, 337
Brookhaven Protein Data Bank
, 308, 314
BROWNIAN
, 361
BuCl, 161
BUILDER
, 365
Bulk solvent region, 128
Bulletin boards, 314
Bump limit, 100
Butadiene, 238, 241
Butane, 242
Butanone, 240
Butene, 242

C2*Alignment
, 354
C*Amorphous Builder
, 354
C2*Analysis
, 354
C2*CASTEP
, 354
C2*CAVEAT
, 354
C2*CDK
, 354
C2*Conformers
, 354
C2*DBAcess
, 354
C2*EXAFS
, 354
C2*Gaussian
, 354
C2*Genetic Algorithms
, 354
C2*Mechanical Properties
, 354
C2*MFA
, 354
C2*MOPAC
, 354
C2*MSA
, 354
C2*Polymorph
, 354
C2*Powder Indexing
, 354
C2*QSAR+
, 354
C2*Receptor
, 354
C2*Visualizer
, 354
C2*X-GEN
, 354
C6H6, 146
C-13 NMR
, 338
CACAO
, 323
CAChe
, 314
CAChe Scientific, 318
CAChe WorkSystem
, 318
CA-Cricket Graph
, 337
CAD Crystallography
, 345
CAD Gene
, 335
CAD/Chem
, 338
CADPAC
, 275, 278, 281, 292, 308, 358, 364
California Scientific Software, 337
Cambridge Crystallographic Data Centre, 21, 308, 364
Cambridge Structural Database (CSD)
, 10, 35, 41, 45, 47, 71, 105, 364
Cambridge University, 308
CambridgeSoft Corporation, 308, 318
Cameleon
, 367
CAMEO
, 375
Camphor, 292
CAPRI
, 355
CarbBank/CCSD
, 326
Carbo index, 91
Carbomethoxyaziridine, 288, 289
Carbon-13 Search
, 328
Carbonic anhydrase, 238
Carboxybenzisoxazole, 161
Car-Parrinello methods, 120, 230
CASREACT
, 329
CASSCF, 275
CAST-3D
, 365
CASTOR
, 367
CASurveyor
, 329
Catalyst
, 365
CATALYST
, 354
Catalyst/Hypo
, 365
Catalyst/Info
, 365
CAVEAT
, 30, 107, 354, 365
CCl4, 152, 166
CCP4
, 376
CD-React
, 325
Central unit cell, 127
Centroid atoms, 73
Cerius2
, 314, 354
CH3CH3, 146
CH3CHO, 148
CH3CN, 146, 237
CH3CO2-, 146
CH3CO2H, 146, 148, 149
CH3COCH3, 146, 148, 149
CH3COOH, 151
CH3NH2, 146, 148, 149
CH3OCH3, 148, 149
CH3OH, 146, 148, 149
CHAIN
, 376
Chain rule, 192
Chapman & Hall, 325
Characterize
, 351
Charge annihilation algorithm, 144
Charge density, 227
Charge flow model, 265
Charge sensitivity analysis, 204
Charge transfer, 128, 157, 158, 202
Charges, 244
CHARMm
, 353
CHARMM
, 139, 140, 168, 299, 314, 349, 366, 371
CHCl3, 152, 153
CHELPG
, 358
Chem3D
, 318
Chem3D Pro
, 318
CHEM-CALC
, 338
chemCLIPART
, 330
ChemCore
, 366
ChemDBS-1
, 366
ChemDBS-3D
, 72, 76, 80, 82, 83, 84, 93, 109
chemDIAGRAM,
330
ChemDiverse
, 366
ChemDraw
, 318
Chemeleon
, 338, 345
chemExhibit
, 330
CHEMFATE
, 334
ChemFinder
, 318
ChemFont
, 332
CHEMGRID
, 368
Chemical Abstracts Services (CAS), 1, 7, 22, 23, 29, 37, 105, 309, 329
Chemical Citation Index
, 339
Chemical Concepts, 370
Chemical Concepts Corporation, 338
Chemical Design Ltd., 319, 349, 366
Chemical information, 314
Chemical information systems, 4
Chemical Pointer File
, 334
Chemical potential, 196, 200
Chemical reactions, 153
Chemical Sciences Graduate School Finder
, 332
CHEMiCALC
, 338
CHEMICALC-2
, 324, 362
ChemInformRX
, 329
ChemInnovation Software, 339
ChemInorganic
, 349
ChemIntosh
, 338
Chemisorption, 168
Chemistry 4D-Draw
, 339
Chemistry conferences, 314
Chemlab, Inc., 320
ChemLib
, 349
ChemMod II
, 318
ChemNovel
, 349
ChemOffice
, 318
Chemometrics, 314
ChemPlus
, 320
ChemPolymer
, 349
ChemPrint
, 317
ChemProtect
, 340
ChemProtein
, 349
ChemQM
, 349
ChemQuery
, 325
ChemReact
, 325
ChemRXS
, 366
chemSAVER
, 330
chemSCENES
, 330
ChemSelect
, 325
ChemStat
, 349
ChemStock
, 332
ChemStructure
, 339
ChemSynth
, 325
chemVISION
, 330
ChemWhere
, 345
ChemWindow
, 338
ChemWord
, 339
ChemWords
, 340
Chem-X
, 71, 72, 109, 319, 349, 366, 375
Chem-X/BASE
, 366
Chem-X/DRAW
, 319
Chem-X/INVENTORY
, 366
CHEM-X/MODEL
, 349
Chem-X/REGISTRY
, 366
Cherwell Scientific Publishing, 330
Chiral molecules, 262
CHIRAS
, 369
CHIRON
, 340
Chloroform, 166
Chloropropane, 243
Chorismate mutase, 155
Chrysene, 167
Circular dichroism (CD), 261, 264
Circularly polarized light (CPL), 261
Civilized Software, Inc., 344
Cl-, 146
Claisen rearrangement, 155, 156
CLASS
, 107
Classical trajectory, 120
Clique, 43, 47, 53, 94
Clique detection, 88, 99
CLIX
, 47
CLOGP
, 355, 367, 374
CLUSTER
, 368
Cluster analysis, 25
Cluster-based selection, 31
Clustering, 75
Clustering databases, 25, 51
Clustering Package
, 367
CMC-3D
, 368
CMR
, 355, 367, 374
CNCH3, 237
CNDO, 359
CNDO/2
, 344
CNDO/S
, 344, 362
CNINDO
, 362
CNINDO/D
, 324
Cobra
, 366
College Chemistry Faculties
, 332
Coloring, 101, 103
COLUMBUS Program System
, 358
Combinatorial library screening, 70, 109
Common origin (CO)gauge, 271, 275
Common subgraph, 6
Comparative Molecular Field analysis (CoMFA), 3, 94, 355, 375
COMPARE-CONFORMER
, 362
COMPASS, 96
Complete active space, 273
COMPOSER
, 355
Compound registration, 72
Comprehensive Chemistry CD Package
, 376
Comprehensive Medicinal Chemistry (CMC) database
, 82, 369
COMPress Division of Queue, Inc., 331
CompuDrug Chemistry Ltd., 344
CompuDrug North America, Inc., 344
Computational biology, 315
Computational chemistry, 303, 316
Computational Chemistry List (CCL), 312
Computer Associates International, Inc., 337
COMPUTER PHYSICS COMMUNICATIONS (CPC) PROGRAM LIBRARY, 363
Computer-aided drug design (CADD), 67
CONCEPTS
, 108
CONCORD
, 10, 23, 33, 37, 45, 46, 83, 97, 98, 109, 355
Condensed phase system, 124
Conduction, 247
CONECT
, 369
Configuration interaction (CI), 132, 135, 166, 237
Conformational analysis, 76
Conformational energies, 239, 240
Conformational equilibria, 151
Conformational families, 75
Conformational flexibility, 11, 44, 69, 72, 74, 76, 97
Conformational sampling, 75
Conformationally flexible 3D database searching, 109
Conformations, 248, 262
CONKAT
, 337
Connection table, 5, 10
CONSISTENT
, 351
Constraints, 80
Constrictor
, 367
ConSystant
, 345
Continuum models, 121
CONVERT
, 362
Converter
, 71, 351
Core-core interaction, 138
CORINA
, 71, 340
Cornell Theory Center, 309, 317
Correlation energy, 220, 221, 222
Correspondence graph, 43
COSMIC force field, 322
Coulomb energy, 196, 198
Coupled differential equations, 273
Coupled perturbed Hartree-Fock, 27
COUSIN database
, 24
Covalent bond division, 130
Covalent bonds, 128
CPKPDB
, 362
CPSLINE PC
, 326
C-QSAR
, 374
Cray Research, Inc., 364
CRC Press
Database, 321
18-Crown-6, 151, 152
CRSTL
, 352
CRYSTAL
, 362
Crystal Cell
, 351
CRYSTAL VISUALIZER
, 327
Crystal Workbench
, 353
Crystallographic Information Files, 346
Crystallography, 315
CSEARCH
, 370
Current Contents
, 339
Current Facts in Chemistry
, 326
Current Literature File
, 369
Customized Polymer Modeling Program
, 349
Cyclobutanes, 290
Cyclohexane, 167, 238, 242
Cyclohexanol, 241
Cyclohexylamine, 242
Cyclopropanes, 277
CYCLOPS
, 346
Cytosine, 141, 147, 148, 149, 251

DARC
, 7
DARC-CHEMLINK
, 326
Data Description Inc., 340
Data Desk
, 340
Database searching, 68
Database structure, 22, 41
Databases, 1, 315, 324, 364
DATALOG
, 334
Datalyst II
, 345
DATAMARINER
, 340
DataMost Corporation, 336
Daunomycin, 41
Daylight Chemical Information Systems, 9, 30, 367
Daylight Toolkits
, 367
De novo design, 44, 108
Decarboxylation, 161, 162
DeCipher
, 351
DeFT
, 226, 228, 229, 359
DEJAVU databases
, 379
DelPhi
, 351
Delta function, 191
DeltaGraph
, 341
DeltaPoint, Inc., 341
DeMon
, 226, 228, 229, 359
Dendrogram, 26
Density functional theory (DFT), 134, 136, 187, 217, 224, 233, 248, 250, 273
Density matrix, 127
Density-function overlap, 3
Depict
, 367
DEREK
, 378
DERMAL
, 334
Dervish
, 367
Derwent, Inc., 326
Derwent Standard Drug File
, 79
Derwent World Drug Index
, 368
Design Science Inc., 344
DESIGN-EASE
, 332, 341
DESIGN-EXPERT
, 332, 341
Desktop Molecular Modeller
, 319
Detector, 264
Deuterioethanol, 291
DFT computer programs, 212
DG II
, 351
DGauss
, 226, 228, 229, 230, 364
DGEOM
, 349, 362
DGPLOT
, 369
Diamond (100) surfaces, 169
DIANA
, 355
Diatomic Molecular Mechanics and Motion
, 323, 331
Dichloroethane, 243
Dictionary of Analytic Reagents
, 325
Dictionary of Drugs
, 366, 370
Dictionary of Fine Chemicals
, 366, 370
Dictionary of Inorganic Compounds
, 325
Dictionary of Natural Products
, 325, 366
Dictionary of Organic Compounds
, 325
Dicyanocyclopropane, 278
Dideuteriobutyrolactone, 290
Dideuteriocyclobutane, 290
Dideuteriooxirane, 280
Dielectric continuum, 121, 136
Diels-Alder reaction, 238
Diethyl ether, 241
Difluoroethane, 243
DIHDRL
, 369
Dihydrofolate, 244
Dihydrofolate reductase (DHFR), 48, 130, 245
Dimethyl dioxane, 242
Dimethyl disulfide, 234
Dimethyl formamide, 152
Dimethylaziridine, 285, 286
Dimethylcyclohexane, 243
Dimethylcyclopropane, 278
Dimethylether, 152
Dimethylthiirane, 283, 284
Dipole moment, 149, 153, 157, 244, 247, 266
Dirac exchange formula, 198
Directed tweak approach, 82
Directory of Graduate Research
, 307
DISCO
, 53, 86, 89, 94, 355
Discover
, 351
DISGEO
, 362
DISMAP
, 324
Dissimilar cluster selection, 31
Dissimilarity search, 30
Distance bound calculation, 81
Distance geometry, 11, 48, 71, 86, 103
Distance keys, 88
Distance matrix, 105
Distance range, 10, 11
Distance-based similarity measures, 32, 39
Distance-distribution measure, 33
DISTMAP
, 368
Distributed Chemical Graphics, Inc., 329
Distributed origin (DO) gauge, 271, 275
Divide-and-conquer approach, 146, 255
Divisive methods, 28
DMol
, 226, 227, 359
DNA, 35, 41, 42, 148, 299
DNA/RNA Builder
, 332
DNMR6
, 362
DOCK
, 34, 35, 42, 44, 46, 47, 48, 49, 98, 103, 368
DOCK
search procedure, 99
DOCK2
, 368
DOCK3.0
, 368
Docking, 32, 45, 46
Dot product, 189
Double-wide sampling, 155, 156
DRAW
, 324, 362
Drug Data Report, 22
Drug design, 46, 87
Drug Discovery Workbench
, 354
DRUGIDEA
, 344
DSolid
, 359
DSTNCE
, 369
DuPont, 47
Dynamic polarizability model, 266

ECEPP2
, 362
ECEPP/3
, 350
Edges, 6, 10
eduSoft, 375
Effective Hamiltonian, 126
Effective potentials, 125
Efficiency of searching, 50
EinSight
, 335
Electron affinity (EA), 201, 207
Electron density, 187, 192, 199, 209, 217, 224
Electron density difference, 164
Electron Diffraction Database
, 328
Electronegativity, 201, 207
Electron-electron repulsion energy, 193, 201
Electronic bulletin boards, 307
Electronic mail addresses, 314, 317
Electronic polarization, 146
Electronic structure calculations, 187, 217
Electronic transitions, 166
Electrophilic attack, 208
Electrostatic complementarity, 48
Electrostatic energy, 219
Electrostatic fields, 3, 32, 244
Electrostatic potential, 54, 197
Electrostatic potential fitted charges, 244
Electrostatic potential similarity, 91
Electrostatic similarity searching, 39
Electrotopographical state indices, 17
ELEUX
, 344
E-mail, 306
EMBL
, 342, 377
Empirical valence bond (EVB) theory, 121, 129, 136, 139, 158, 168
Enantiomers, 262
EndLink
, 332
EndNote
, 332
EndNotePlus
, 332
Endothelin, 98
Energy decomposition method, 131
Energy functional, 219
Enriching Quantum Chemistry with Mathcad
, 341
Entropy
, 338
Environment templates, 74
Environmental Fate Data Bases
, 334
Enzymatic reaction, 168
EnzymeKinetics
, 323
Enzyme-substrate systems, 128
Enzymix
, 354
Equations of motion, 232
EQUIL
, 332
EROS
, 340
ESOCS
, 359
ESP
, 323
Essential points, 48
ESTAR
, 362
Ethane, 236
Ethanol, 241
Ethyl formate, 240
Ethylene, 236, 238
Ethylene glycol, 239, 292
Euclidean distance, 20
Eukaryotic Promoter Database
, 326
Euler equation, 195
Euler-LaGrange equations, 195, 201, 206
EUREKA
, 367
European Communities Joint Research Centre, 26
Exchange energy, 198, 220, 221, 222
Exchange-correlation energy, 201, 209
Exchange-correlation functional, 136, 205
Excitation energy, 272
Excited solute, 133
Excited states, 132, 134, 273
Exographics, 338
Explicit solute-solvent interactions, 128
Explicit solvent effects, 122
EXPOD
, 374
Expressionist
, 341
Extended Hückel Theory (EHT), 318, 323, 357
External potential, 205
EXTOIN
, 324
Extremals of functionals, 193

F3D
, 340
Fachinformationszentrum (FIZ) Karlsruhe, 327
FACTANAL
, 362
Falcon Software, 376
FAMILY
, 53
FARMmCHARMm
, 353
FCD-3D
, 369
FCI
, 363
Felix
, 351
FIG.P
, 335
Field-based approaches, 54
File transfer protocol (ftp), 306
Fine Chemicals Database (FCD)
, 101
Fingerprint
, 367
Fingerprints, 9
FISIPL
, 369
Fixed partial charge model, 265
FLEX
, 370, 380
Flexible 3D similarity searching, 44, 45
Flexible 3D substructure searching, 11
Flexible molecules, 83
Flexible searching, 13
Flexifit
, 366
FlexModel
, 355
Floating basis set formalism, 267
FLOG
, 48, 103
Fluoropropane, 243
FlyBase
, 326
Fock matrix, 127, 137, 228
Folate, 244
Folding, 9
FOLIO Views
, 337
Force field parameter, 159
Force field weaknesses, 231
Force fields, 126, 212, 273
Formaldehyde, 166, 237
Formic acid, 240
Formula key, 78
FORTICON8
, 324, 362
FORTICONMAC
, 324
FOUNDATION
, 43
Fourier transform interferometer, 264
Fraga relations, 198
Fragment substructures, 18
Fragment-based search, 24
Fragment-based similarity searching, 19
Fraser Williams Scientific Systems, Ltd., 318
Free energies of hydration, 146, 157
Free energies of solvation, 144
Free energy perturbation (FEP), 145, 151, 155, 158, 159
FREQ86
, 274
FRODO
, 376
Frozen density technique, 146, 170
Frontier orbital theory, 203, 208
Fukui function, 203
Fukui refractivity indices, 208
Functional, 188
Fuzzy-match searching, 23

GAMESS
, 359, 362
GAMESS-UK
, 362
Gardner's Chemical Names and Trade Names database
, 332
Gauge-independent atomic orbitals (GIAO), 271, 274
GAUSS
, 341
GAUSS2
, 323
Gaussian
, 139, 154, 156, 218, 226, 227, 229, 230, 274, 277, 281, 324, 362, 364
Gaussian 92/DFT
, 360
Gaussian functions, 209
Gaussian, Inc., 360
Gaussian-type orbitals, 225
GCG Package
, 376
GDFB
, 361
GDFMOL/GDFMD
, 361
GEMINI
, 367
GEMM
, 371
GenBank
, 326, 342, 367, 377
Generalized Born models, 121, 153
Generalized torsional angle, 36
Generic TOPFRAG
, 326
GENESEQ
, 342
Genetic algorithm, 55, 315
Genetics Computer Group, Inc., 376
GeneWorks
, 342
GENIE
, 374
GENIE/SMARTS
, 367
geNMR
, 327
Geometric searching, 10, 11, 27
GEPOL
, 362
Gesellschaft für Technisch-Wissenschaftliche Software mbH, 328
Gibbs-Duhem equation, 202
Global hardness, 202, 203
Global LaGrange multipliers, 195
Global similarity measure, 14, 33
Global softness, 202, 203
Gluplot
, 342
Glycine dipeptide, 247, 248, 249, 250
Glyoxylic acid, 240
GMELIN
, 329
GMMX
, 322
Gnomonic projections, 91, 104
Gopher
, 306, 377
GPMAW
, 321
Gradient corrected functionals, 189, 223, 228, 229, 233, 234, 254
Gradient correction, 199
Gradient operator, 189
Gradient-corrected DFT, 240, 246, 254
GRADSCF
, 360
GRAMPS
, 348, 371
GRANNY
, 348
Grant Tracker
, 332
Graph theory, 2, 6, 27
GraphPad Software, 346
GRASP
, 371
GRID
, 47, 103, 108, 350, 362
Grid-based approaches, 54
GROMOS
, 299, 315, 350, 367
Ground state density, 220
GROUPBUILD
, 354
GroupServer
, 318
GSTAT
, 365
Guanine, 147, 148, 149, 251

H2ION
, 323
Hall Associates Consulting, 334
HAM/3
, 324
Hamiltonian, 124, 194
Hammond postulate, 160
HAMOG
, 319
Hampden Data Services, Ltd., 328
Hartree-Fock exchange operator, 189
Hartree-Fock self-consistent field (HF-SCF), 127, 134, 211, 218, 224, 240, 246, 248, 250
Hartree-Fock wavefunction, 123, 132
Hashing, 9
Hawk Scientific Systems, 344
HAZARDEXPERT
, 344
HelicalWheel
, 377
Hellman-Feynman forces, 230
Henry's Law Constant Program
, 334
Hessians, 229
Heterolytic bond cleavage, 121, 154
Heuristic estimate of synthetic proximity, 53
Hewlett-Packard, 309
Hexadecane, 156
Hexamethylphosphoramide, 161
Hierarchical clustering, 26
Hierarchical divisive methods, 28
Hierarchical Organization of Reactions through Attribute and Condition Eduction (HORACE), 52
Higher Dimension Research, Inc., 349
High-performance computing, 315, 317
HINT
, 375
HiQ
, 342
Histamine H1, 72
Hitachi Software Engineering America, Ltd., 342
Hits, 84
HIV-1 protease inhibitors, 46, 95, 108
HIV-protease, 35, 47
HMO
, 323
Hohenberg-Kohn theory, 200, 217, 219
Homology
, 351
HONDO
, 360, 363
HONDO-8
, 361
HOOK
, 354
HPLC-METABOLEXPERT
, 344
Hückel molecular orbital (HMO), 323
Human Genome Project, 309
Hybrid clustering, 52
Hybrid QM/MM potential, 143
HYCOIN
, 361
Hydrogen bonds, 48, 140, 142, 156, 211, 218, 222, 223, 225, 235, 245, 248, 251, 253, 254, 289
Hydrogenation reactions, 236
Hydrophobic centers, 72, 88
Hydrophobic effects, 156
Hydrophobic fields, 3, 32
HyperChem
, 130, 139, 315, 319
Hypercube Inc., 130, 319
HyperNMR
, 320

IBM, 309, 360
ID Patent Fast Alert
, 370
Idea structures, 109
Iditis
, 367
ILIAD database
, 366
Imdad
, 330
Imidazole, 146
Imperial College, 309
Index Chemicus
, 339
Indiana University, 309
Indiana University-Purdue University at Indianapolis Chemistry Department, 309
INDO, 357, 359
INDO-SCRF, 167
Induced dipole moments, 148, 149
Induced dipole-induced dipole interactions, 133
Influenza-virus hemagglutin, 47
InfoChem database
, 366
InfoChem GmbH, 325
InfoMetrix, Inc., 335
Infrared spectrometers, 263
Inorganic Crystal Structure Database
, 327
Inositols, 239
InPlot
, 346
Insight II
, 375
Insight Xpress
, 351
Insight/Discover
, 350
InStar Software AB, 320
InStat
, 346
InStep
, 335
Institute of Scientific Information (ISI), 339
Integrated Graphics, 345
Integrated Risk Information System database
, 332
IntelliGenetics, Inc., 342
InTend
, 346
Interatomic distance matrices, 39
INTERCHEM
, 362
Intermediate neglect of differential overlap (INDO/S), 166, 357
Intermolecular similarities, 39
International Union of Crystallography, 310
INTERNET, 306
Internet Gopher Developers, 377
InterNIC, 310
Interphases
, 351
Intrinsic reaction coordinate (IRC), 154, 156, 161
Inverse functional derivative, 192
Ionization potential, 201, 207
IR Mentor
, 332
IR Search
, 328
IR SearchMaster
, 332
IRMA
, 351
Isomorphic graph, 6
Isopropanol, 241, 241
Isopropylamine, 242
ISIS
, 368
ISIS/3D
, 74, 80, 82, 83, 84, 315
ISIS/Base
, 368
ISIS/Desktop
, 368
ISIS/Draw
, 368
Isoxazole, 163
Iterative design process, 68
IvorySoft Scientific Software, 327
IVTANTHERMO
, 328

Jandel Scientific Software, 336
Japan Association for International Chemical Information, 379
Jarvis-Patrick method, 30
JETNET
, 363
JG-365, 47
JMP
, 333
Journal of Chemical Education: Software
, 341
Journal of Computer-Aided Molecular Design
, 3
Journal of Medicinal Chemistry
, 3
Journal of Synthetic Methods
, 23
Journal of the American Chemical Society
, 332

Kekulé
, 342
Key search, 79
Keys, 22
KGNGRAF
, 361
KGNMD
, 361
KGNMOL
, 361
KGNNCC
, 361
Kinemage
, 310, 331
Kinetic energy, 193, 196, 198, 201, 219, 231
KinWorks
, 341
Klotho Biochemical Compounds Database
, 310
Kohn-Sham orbitals, 136, 218, 220
Kohn-Sham theory, 136, 204, 225

LabADVISOR database
, 332
Labeled graph, 6
Laboratory Software Ltd., 339
LABSWARE
, 344
LabSystant
, 323
LabVIEW
, 315, 342
LabVision
, 317, 355
LabWindows
, 315, 342
LaGrange multipliers, 194, 200, 231
Lance-Williams matrix-update formula, 27
Largest indentical regions, 53
LaTex
, 347
Latticepatch
, 377
Lawrence Livermore National Laboratory, 310
LAZY
, 349
Lead generation, 96, 101
Leader algorithm, 29
LEAPFROG
, 355
Lederle algorithm, 34
Lederle Laboratories, 22, 34
Legion
, 370
Lennard-Jones terms, 125, 138, 140, 142, 212
LHASA
, 52, 53, 377
Ligand alignment, 95
Ligand superposition, 91
Ligand-receptor complex, 46
LIGHT, 371
Linear combination of atomic orbitals (LCAO), 226
Linear dichroism, 264
Linear response theory, 132, 148
Link atoms, 129, 170
Local functionals, 189, 223
Local hardness, 192, 203
Local LaGrange multiplier, 195
Local reaction field method, 128
Local consistent field method, 130
Local similarity measure, 14, 33, 39
Local softness, 192, 203
Local Spin Density Approximation (LSDA), 221, 224, 235, 236, 237, 240, 246, 254
Localized bond orbital, 130
Localized molecular orbital model, 266
Localized orbital/local origin (LORG), 272
Locally distributed origins gauge model, 266
Logica UK, Ltd., 340
LogiChem, 334
LOGKOW
, 333, 334
London atomic orbitals, 271
Long-range Coulombic interactions, 128
LOOK
, 331
Lorentzian lineshape, 282, 284, 286, 287, 289
Low density lipoprotein (LDL), 96
LUDI
, 108, 351
Lysis reaction database
, 325
Lysozyme, 129, 168

MACCS
, 1, 21, 70
MACCS-3D
, 68
MACCS-II
, 22, 80, 368
MacDNASIS
, 342
MacLogP
, 374
MacMimic
, 320
MacroModel
, 310, 348, 351
MAD
, 367
MAGE
, 331
MAGIC
, 340
Magnetic field perturbation (MFP) theory, 267, 275
Magnetic properties, 274
Malonaldehyde, 222, 224
Manugistics, Inc., 336
Many-body perturbation theory (MBPT), 135
Maple
, 343
MARDIGRAS+
, 355
Marinlit
, 327
MARPAT
, 329
MASCA
, 322
Mass parameters, 232
Massively parallel processors, 40, 51
MASTERFILE database
, 374
MatchMaker
, 355
Materials Science Citation Index
, 339
Mathcad
, 343
Mathcad, Inc., 343
Mathematica
, 310, 343
MathType
, 343
The MathWorks, Inc., 343
MATLAB
, 343
Maximal common subgraph, 6
Maximal common substructure (MCS), 19, 24, 33, 42, 52, 53
Maximum dissimilarity selection, 31
Maximum similarity, 51
MAXWELL
, 362
Maxwell Online, 325
Maybridge93
, 367
MCQUB
, 139
MCSCF, 156
MD Display
, 362
MDDR-3D
, 369
MDL Information Systems, 1, 19, 21, 22, 52, 68, 310, 315, 368
mdXvu
, 362
MedChem94
, 368
MedChem/BioByte QSAR Database
, 310
MEDIT
, 352
MEDLARS
, 329
MEDTOOL
, 340
Megalon S.A., 339
MELD
, 361
Menshutkin reaction, 159
MEP-fitted charges, 149
Merck indexes
, 48
Merck Modeling Force Field (MMFF), 353
Merlin
, 367
MERLIN
, 374
MerlinServer
, 367
Mero dyes, 166
METABOLEXPERT
, 344
METALYSIS
, 369
Methane, 237
Methanol, 166
Methods in Organic Synthesis (MOS)
, 324
Methoxycyclohexane, 241, 243
Methoxytetrahydropyran, 242
Methyl acetate, 240
Methyl ethyl ether, 241
Methyl formate, 240
Methyl lactate, 292
Methyl radical, 237
Methyl vinyl ether, 241
Metropolis Monte Carlo, 119, 139, 166
MicroChem
, 320
MicroQSAR
, 333
MidasPlus
, 370
MINDO/2, 129
MINDO/3, 357
Minimum energy reaction path (MERP), 154
Minitab
, 315, 334
Minnesota Supercomputer Center, Inc., 373
MINP
, 352
MLab
, 344
MLDC8
, 324, 362
MM2
, 318, 324, 352, 362
MM3
, 352, 355, 362
MMX force field, 322
MNDO, 121, 135, 138, 140, 143, 151, 299, 357
MNDO
, 324, 362
MNDO93
, 364
MNDOC
, 362
MOBY
, 320
Mocha
, 336
MODDE
, 375
MODEL
, 352
Modeler
, 331
Modeling reactions, 235
MOIL
, 352
moil-view
, 352
MOLCAD
, 355
MOLCAS
, 361
MOLCAS-1
, 361
MOLCONN-X
, 17, 334
MOLDEN
, 361, 362
MOLDRAW
, 324
Moldy
, 352
Molecular Analysis Pro
, 321
Molecular Animator
, 331
Molecular Applications Group, 330
Molecular Arts Corporation, 330
Molecular biology sequence database
, 310
Molecular connectivity indices, 16
Molecular Discovery Ltd., 350
Molecular dynamics (MD), 119, 134, 135, 152, 158, 166, 230, 231, 233, 239, 299, 316
Molecular electrostatic potential (MEP), 3, 42, 88, 149, 244
Molecular fields, 55
Molecular geometries, 233
Molecular graphics, 85, 92, 310, 330, 370
Molecular Graphics
, 331
Molecular mechanical force fields, 244
Molecular mechanical region, 123
Molecular mechanics (MM), 120, 126
Molecular modeling, 303, 316, 317, 348
Molecular Modeling Pro
, 321
Molecular orbital (MO) theory, 122
Molecular Presentation Graphics (MPG)
, 344
Molecular properties, 39
Molecular shape, 92, 103, 105
Molecular shape indices, 17
Molecular silverware
, 355
Molecular similarity, 88, 94, 95
Molecular Simulations Inc., 310, 353, 365
Molecular Spreadsheet
, 355
Molecular volume, 88, 93
Molecules
, 331
Molecules-3D
, 330
MOLFIT
, 362
MOLGEN
, 321
MOLIDEA
, 344
Møller-Plesset second order (MP2), 218, 224, 240, 246, 248, 250, 270, 272, 283
MOLSCRIPT
, 372
MOLSIMIL-88
, 363
MOLSVMAC
, 324
MOLVIB
, 324
MOLVIEW
, 324
MOLY-86
, 362
MOLYROO
, 324
Momentum-space electron densities, 3
Monothetic divisive methods, 28
Monte Carlo (MC), 119, 122, 135, 145, 152, 153, 165
MOPAC
, 23, 139, 316, 318, 323, 324, 345, 361, 362
MOPC
, 324
MOPLOT2
, 362
MORASS
, 378
MORATE
, 363
MOS
, 362
Mosaic
, 307, 378
MOSAIC
, 43, 44
MOTECC: Modern Techniques in Computational Chemistry
, 361
MPBPVP
, 334
mpp
, 345
MPROP
, 292
MS
, 362
MS Calculator
, 338
MSEED
, 362
MSP
, 378
Mulliken
, 318
Mulliken population, 153, 157, 158, 163
MULTIC
, 351
Multiple conformations, 109
MVT-101, 35, 47

NADPH, 244
NameExpert
, 339
NAMOD
, 324
NanoVision
, 332
Naphthalene, 167
NASITE
, 342
National Cancer Institute, 19, 26, 29
National Center for Atmospheric Research, 317
National Center for Biotechnology Information, 326
National Center for Supercomputing Applications, 311, 317
National Institute of Standards and Technology, 328
National Institutes of Health, 311, 326, 329
National Instruments, 342
National Library of Medicine/Environmental Protection Agency, 329
NBRF-PIR
, 367
NCSA Contours
, 378
NCSA Image
, 378
NCSA ImageTool
, 378
NCSAdisco
, 363
NDDO, 135
NDDO/1, 357
Nearest neighbors, 13, 30
Nemesis
, 322
NetBiochem, 311
Netropsin-B, 35, 41
Netscape
, 307, 311
Networks
, 351
Neural Computer Sciences, 345
Neural networks, 316
Neuroscience Citation Index
, 339
NeuRun for Applications
, 345
NEWCRYST
, 365
NEWHEL92
, 369
Newspage, 311
Newton-Raphson minimizer, 92
Newton's equations of motion, 126
Newzmat
, 360
NH3, 148
NHDT, 276
NIST Crystal Data File
, 327
NIST Structures and Properties Database
, 328
NIST/NASA/CARB Biological Macromolecule Crystallization Database
, 328
NITRO
, 355
Nitroaniline, 149
NM Display
, 362
N
-Methylacetamide, 146, 148, 149, 240
N
-Methylformamide, 240
N
-Methylpiperidine, 242
NMR Analysis
, 351
NMR Database
, 351
NMR Workbench
, 353
NMR1
, 355
NMRchitect
, 351
NMR*Compass
, 353
NMR*Pipe
, 353
NMRZ
, 355
N.N.Charge
, 332
Nodes, 6, 10
NOEL
, 362
NOEMOL
, 362
Nonbonded list, 129
Nonheirarchical clustering, 29, 31
Nonlocal functionals, 189, 223
Nonlocalized molecular orbital model, 266
Normal vibrational mode, 269
NorMode
, 324
North Carolina Supercomputing Center, 311
Northern Illinios University, 306, 311
NP-complete computational problems, 33, 48
NQRS database
, 379
NQRS PC SEARCH
, 379
NRL3D Database
, 311
Nuclear kinetic energy operator, 267
Nuclear velocity perturbation velocity-gauge formalism, 267
Nuclear-electron attraction energy, 193, 196, 198
Nucleic Acid Database
, 328
Nucleic acids, 126, 262
Nucleophilic addition reaction, 299
Nucleophilic substitution reactions, 158
Nucleotide bases, 147, 251
Numerical functions, 209, 230
NUMOL, 226, 230

O
crystallographic program, 311, 316, 378
Ohio Supercomputer Center (OSC), 306, 312, 317, 332
Omega
, 378
OncoLogic
, 334
Onsager reaction, 121
OpenMolecule, 372
Optical activity, 261
Optical rotatory dispersion (ORD), 261
Optically pure, 262
Optimized potentials for liquid simulations (OPLS), 123, 139, 141, 143, 147, 152, 155
ORAC
, 369
ORACLE
, 379
OREX ExpertSystem
, 335
Organic chemistry, 316
Organometallic chemistry, 316
Organometallic Compound Database
, 370
Organon, 41
ORGSYN
, 369
Origin
, 332
Origin gauges, 271
Origin independent rotatory strength, 271
ORTEP_for_Mac
, 332
OSAC
, 369
Oscillator strength, 262
Outokumpu HSC Chemistry
, 345
Overlap volume, 91
OVID
, 3, 91
Oxford Electronic Publishing, 319
Oxford Molecular, 318, 322, 366
Oxiranes, 278
Ozone, 222

Pacific Northwest Laboratory, 357
Pairwise-distance descriptors, 15
PAP
, 362
Papain, 168
Parallel algorithms, 170
Pariser-Parr-Pople (PPP), 129, 139, 359
Partial charge, 137, 149
Path lengths, 34
Path number sequence, 15
Path numbers, 15
PC-Chemmod
, 319
PCDISPLAY
, 322
PC/GENE
, 342
PC-HYDRO
, 334
PCILO/2
, 324
PCILO3
, 362
PC-KOC
, 334
PC-Mendeleev
, 323
PCMODEL
, 322
PCModels
, 367
PCNONLIN
, 332
PC-PROT+
, 322
PC-TAMMO+
, 322
PDB-Browse
, 369
PDM88
, 362
PDM93
, 363
PeakFit
, 332, 336
PEFF
, 362
Pentadiene, 238
Pentenal, 157
PEPA
, 362
PepPlot+
, 377
Peptide bond rotation, 152
Peptide Companion
, 321
PEPTIDESTRUCTURE
, 377
Periodic boundary conditions, 127, 246
Periodic_Table_for_Mac
, 332
Periodic Table Stack
, 341
Personal Bibliographic Software, Inc., 346
Personal computers, 317
Perturbation expansion, 191
Pesticide Facts database
, 332
PETRA
, 340
Pfizer, 22, 26, 30
Pharmacophore centers, 86
Pharmacophore generation, 85, 108
Pharmacophore map, 12, 44, 53
Pharmacophore model, 6, 89, 90
Pharmacophore query, 70, 74
Pharmacophore searches, 72
Pharmacophore validation, 85, 92
Pharmacophore Identification
, 349
Pharmacophores, 68, 78, 79, 108
PHARMSEARCH
, 345
Phase Diagram
, 351
Phospholipase A2, 168
PHOTO
, 361
Photoelastic modulator, 263
Physical Properties Data Base
, 334
Physicochemical parameters, 52
PIFF
, 362
PileUp
, 377
PIMMS
, 367
Piperidine, 242
PIR
, 342, 377
Pirouette
, 335
Pittsburgh Supercomputing Center, 312, 317
pKa, 151
pKa Database
, 321
PKALC
, 344
Plane Wave
, 359
Plane waves, 209, 226, 233, 246
PLH-91
, 361
PLT2
, 371
PLTCOR
, 345
PLUTO
, 365
PM3, 135, 138, 143, 169, 357
PMD
, 312
POCKETT
, 362
Poisson equation, 197, 199, 228
Polaris
, 354
Polarizable solvent model, 167
Polarizability, 212
Polarization, 244
Polarization differential, 152, 153
Polarization energies, 148
Polarized solute, 132
Poling function, 75, 77
POLLY
, 375
Poly Software International, 335
POLYATOM
, 324
Polyatomics Research Institute, 360
Polygraf
, 354
Polymerizer
, 351
Polymers, 262, 316
POLYMOL
, 363
Polypeptide models, 247
POLYRATE
, 362, 363
Polythetic divisive methods, 28
Polyview
, 378
Pool, Heller, and Milne, Inc., 347
POSSUM
, 355
Potential of mean force (PMF), 151, 159, 161
Powder Diffraction File,
328
PowerSearch
, 317
PPP-MO
, 362
PREKIN
, 331
Prescience, 341
PRESTO
, 362
Printing Package
, 367
Prism
, 346, 351
Procheck
, 369
Pro-Cite
, 346
PRODEN, 362
Product-moment correlation coefficient, 21
Pro-Explore
, 367
Professional Polygraf
, 354
Profiles-3D
, 351
PROGNOSYS
, 337
Project Seraphim, 322, 341
ProjectLeader
, 318
PROLOGD
, 344
PROLSQ
, 351, 376, 379
Prometheus
, 353
PRONET
, 361
Property field comparisons, 79
PROPHET
, 353
Propionaldehyde, 240
Pro-Quantum
, 367
Pro-Simulate
, 367
PROSITE
, 342
ProStat
, 351
PROTEAN II
, 324
PROTECT
, 378
Protecting Groups
, 324
Protein crystallography, 315
Protein Data Bank (PDB)
, 71, 369
Protein docking problem, 48
Protein Expert
, 333
Protein Identification Resource
, 325
Protein Predictor
, 332
Protein Science
, 310, 312, 331
Protein sequences, 311, 312
Protein simulations, 123
Proteins, 126, 145, 148, 168, 247
PROTEINS
, 362
PROTEP
, 355
Proteus Molecular Design Ltd., 353
Proton transfer, 165
Prous Science Publishers, 326
PSDD
, 362
Pseudohalogen atoms, 130
Pseudopotental methods, 170
PS-GVB
, 363
PSI International, Inc., 342
PSI77
, 349, 362
PSI88
, 364
PsiBase
, 328
PsiGen
, 328
Psi-Plot
, 335
Pyridone, 149, 153

QCFF/PI, 166, 362
QCLDB
, 379
QCPE, 139, 312, 323, 361
QMDCP
, 361
QM/MM partitioning, 170
QREG
, 374
QSAR, 32, 94, 318, 336, 340
QSAR parameters
, 324
QSAR-PC
, 335
QSPR
, 351
QSPR-Polymer
, 354
QUANTA
, 353
QUANTA/CHARMm
, 316, 353
QUANTA/NMR
, 353
QUANTA/StAR
, 354
Quantitative Structure-Activity Relationships
, 3
Quantitative structure-property relationships, 333, 374
QUANTRA/Bones
, 353
Quantum Barrier
, 341
Quantum Chemistry, 322, 356
Quantum Consistent force field (QCFF/ALL) method, 128, 139
Quantum mechanical (QM) methods, 120, 122
Quantum mechanical region, 123
Quantum mechanical tunneling, 165
Quantum mechanics, 195
Quantum Monte Carlo, 222
QUASAR
, 346
Query molecule, 6, 22
Query pharmacophore, 11, 14
Query substructure, 6, 9, 12
QUEST
, 139, 364
QUEST3D
, 365
Questel, 326

Radial distribution function, 247
RAIN
, 346
Random phase approximation (RPA), 272, 275, 278
Ranked 3D substructure search, 40
RasMol
, 332, 372
RASTER3D
, 372
Rational drug design, 69
Rattler
, 367
Rayleigh-Schrödinger perturbation theory, 268, 269
REACCS
, 19, 21, 23, 52, 369
REACCS-JSM
, 369
Reaction coordinate, 159, 168
Reaction field, 121
Reaction similarity searching, 19, 51
Reactivity index, 203
REATOM
, 361
RECEPTOR
, 355
Receptor site, 45
Receptor-constrained 3D screening, 98
Reciprocal Nearest Neighbors, 28
Reduced graphs, 23
Reducibility property, 28
Reference Manager
, 346
REGISTRY
, 329
Relocation methods, 29
REPLACE
, 351
Research Information System, 346
ResearchStation
, 339
Restriction Enzyme Database
, 326
RETRIEVE
, 327
RIAS
, 363
Ribbons
, 373
Rigid structures, 45
RING
, 324
Ring centroids, 72
Ring current model, 265
RIS
, 351
Root mean square difference (RMSD), 3, 41, 76, 80, 104, 142
Rotatory strength, 261, 265, 270, 276, 280
RRKM
, 362
Rubicon
, 367
Rule-based structure generation, 72

Sabre
, 319
Sadtler Molecular Structure Search Software
, 328
SAMPLS
, 362
San Diego Supercomputer Center, 312, 317
SAS Institute Inc., 316, 333
Scaling, 192, 229
SCARECROW
, 254
SCHAKAL
, 333
Schrödinger equation, 123, 136, 194, 201, 217
Schrödinger, Inc., 363
Schrödinger theory, 187
SciAn
, 373
SCIBASE
, 324
Science Citation Index
(SCI), 339
Scientific Information Service Inc., 327
Scientific Software, 340
Scientific Word
, 346
Scientific WorkPlace
, 347
SciFinder
, 329
SciLogP
, 335
SciLogW
, 335
SciPolymer
, 335
SciPredictor
, 335
SciVision, 335
SciWords
, 338
SciWords for Agriculture
, 347
SciWords for Biology
, 347
SciWords for Chemistry
, 347
SciWords for Environment
, 347
SCOP
, 312, 369
Scoring function, 46
Screen dictionary, 9
Screening search, 7
Screenout, 7
SEAL
, 362
Search speeds, 79
Search/Compare
, 351
Search-time-defined atom typing, 74
SegMod
, 331
Selector
, 370
Self-consistent field (SCF), 211
Self-consistent reaction field (SCRF), 122, 124, 146, 147, 153, 155, 159, 160
Semichem, 357
Semiconductors, 233
Sequential Agglomerative Hierarchical Nonoverlapping methods (SAHN), 26
Serena Software, 322
Serratus
, 367
SHAKE algorithm, 232
SHAPE
, 380
Shape similarity, 41, 46, 54, 91
Shape-constrained searches, 103
Si(100) surface, 168
Sialic acid, 47
SIBFA
, 362
SIGFILE
, 374
SigmaPlot
, 336
SigmaScan/Image
, 336
SigmaStat
, 336
Sigmatropic shift, 238
Signature similarity, 105
Silicon Graphics, 312
SILMUT
, 324
SIMCA-IPI
, 375
SIMCA-R
, 375
Similar property principle, 26
Similarity coefficients, 20
Similarity criteria, 56
Similarity measure, 4
Similarity searching, 1, 2, 10, 13, 14, 30, 31, 51
Simulated annealing, 47, 316
Simulated annealing
, 351
SIMULINK
, 343
SIMVOL
, 362
SIMVOL/PLTSIM
, 324
Single-atom fragments, 8
Single-pass methods, 29
Singletons, 29
SIRIUS
, 361
Site point, 94
Sketcher
, 351
Slater determinant, 123
Slater-type orbitals (STO), 209
SM4-SRP, 156
SMARTS
, 367
SMILES
, 70, 109, 367
SMILES Notations
, 334
SmithKline Beechham database
, 46
Smoothing function, 127
SN1 reactions, 160
SN2 reactions, 119, 145, 154, 158, 160
Softron Substructure Search System
, 328
SoftShell International 338
Software, 303, 317
Software for Science
, 312
Solids Adjustment
, 351
Solids Builder
, 351
Solids Docking
, 351
Solids Refine
, 351
Solids Simulation
, 351
SolidState
, 351
Solute polarization, 156
Solute region, 121
Solute-solvent interaction Hamiltonian, 127, 131, 137, 144
Solute-solvent polarization, 131, 133
Solvation energy, 144, 167
Solvatochromic spectral shifts, 132, 165, 167
SOLV-DB
, 334
Solvent cage, 133
Solvent effects, 153
Solvent polarization effects, 120, 125, 130
Solvent region, 121
Solvent reorganization energy, 130
Solvent spectral shift, 134
Solvent-induced charge separation, 160
SPARTAN
, 354
SPASMS
, 316
SPC water model, 244
Specific reaction parameterization, 156
SPECINFO
, 329, 370
SPECS database
, 366
SpecTool
, 332
Spectral shifts, 166, 167
Spectro
, 358
SPERM
, 104, 106
SPERM method, 41, 55
Spherical cutoff, 127
SPHGEN
, 368
Spin densities, 220
Spiro[4,4]nonane-1,6-diol, 294
Spresi
, 368, 370
Springer-Verlag, 320
SQUASH
, 379
SRS II
, 323, 331
SST
, 52
Standard Drugs File
, 366
Standardization, 19
STARLIST
, 374
STAT-EASE, Inc., 341
STATGRAPHICS Plus
, 336
STATISTICA
, 336
Statistical ensemble averaging, 123
Statistics, 316, 333, 374
StatMost
, 336
StatSoft, 336
STEREO
, 369
Steric and Electrostatic ALignment (SEAL), 55, 56
Steric complementarity, 48
Steric fields, 3, 32
STERIMOL
, 324
STN EXPRESS
, 329
STN International, 329, 365
Stochastic boundary, 128, 168
Stochastic searching procedures, 55
Stored matrix, 27
Structural descriptors, 15
Structural-fragment descriptors, 15
Structure generation, 70
Structure Image
, 351
Structure searching, 2, 6
Structure similarity searching, 19
Structure Solve
, 351
Structure-activity relationship (SAR), 3, 68
Structure-based design, 98
Subgraph isomorphism, 6, 7, 9, 10
Subsimilarity searching, 19, 22, 24
Substituent Database
, 349
Substructure database, 73
Substructure mappings, 109
Substructure searching, 2, 5, 9, 10, 12, 13, 79
SUPER
, 91
Supercomputer Computations Research Institute, 373
Superimposition, 46
Supersimilarity searching, 22
Superstructure search, 22
SURFACE
, 376
Surface terms, 193
Surface-constrained all-atom solvent (SCAAS), 158, 166
SWISS-PROT
, 312, 326, 342, 367, 377
SYBASE
, 347
Sybase, Inc., 347
SYBST
, 362
SYBYL
, 95, 312, 316, 317, 355, 375
SYBYL Line Notation (SLN), 74
SYBYL/3DB
, 80
SYNLIB
, 329
Synopsys database
, 366
Synopsys Scientific Systems Ltd., 324
Synthesis design, 52
Synthia
, 351
SynTree
, 323, 331

TableCurve
, 332, 336
Tanimoto coefficient, 20, 22, 29, 36, 39, 45
Target receptor, 68
Target structure, 2, 13, 14, 24, 30, 35, 40, 41, 50
Tautomeric equilibria, 153
Taylor expansion series, 268, 269
TCI Software Research, 346
TDS Numerica
, 333
Technical Utilization Corporation, Inc., 352
Tesselated icosahedron, 41
Tetrodotoxin, 106
THEILHEIMER
, 369
THEORIST, 343
Thermodynamic and Physical Properties database
, 323
Thermodynamic cycle, 144
Thermodynamic properties, 119
Thiiranes, 283
Thiomethanol, 234
Thomas-Fermi (TF) Model, 195
Thomas-Fermi-Dirac (TFD) model, 198
Thor
, 367
ThorMan
, 367
THOR-R/W
, 374
ThorServer
, 367
Three-dimensional chemical structures, 10
Three-dimensional clustering methods, 56
Three-dimensional databases, 1, 31, 68
Three-dimensional grid, 3
Three-dimensional keys, 88, 93
Three-dimensional maximal common substructure, 33, 53
Three-dimensional molecular similarity index, 91
Three-dimensional QSAR, 3, 95
Three-dimensional screens, 78
Three-dimensional similarity searching, 32
THREEDOM
, 362
Threshold similarity value, 22
Thromboxane synthetase, 79
Thymidylate synthase (TS), 101, 108
Thymidylate synthase inhibitors, 102
Thymine, 147, 148, 149, 251, 252
TIP3P water model, 121, 140, 161, 244
TIP4P water model, 244
TOPDRAW
, 337
TOPKAT
, 336
TOPKAT/EA
, 336
TOPKAT/TPS
, 336
TOPMOST
, 336
Topological indices, 15, 16, 17
Topological screen, 80
Topological sequences, 15
Topological torsion fragment, 8
Topology, 6
Torsional angle, 35
Torsional dissimilarity coefficients, 36
Torsional fitting, 80
Torsional tweak methodology, 82
TOXNET
, 329
Transcription Factor Database
, 326
Transition moments, 265, 266
Transition state geometry, 156
Transition states, 211, 237
Transmission Control Protocol/Internet Protocol (TCP/IP), 306
Transputer networks, 51
TRIAD
, 366
TRIAD Base
, 355
TRIAD NMR
, 355
Triangle descriptors, 103
Trinity Software, 323
Triosephosphate isomerase (TIM), 168
Triplet descriptors, 107
Tripos, Inc., 1, 22, 45, 317, 355, 370
Trypsin, 168
Tsar
, 367
TSCA database
, 18, 368
Turbomole
, 359
TurboNMR
, 351
Two-dimensional chemical structures, 5
Two-dimensional connection table, 10, 68, 70
Two-dimensional databases, 1, 14, 68
Two-dimensional fragment screens, 24
Two-dimensional similarity searching, 18, 21, 23, 50
Two-dimensional topological queries, 108
Two-electron integrals, 228

UHBD
, 354
Umetri AB, 375
UniChem
, 312, 364
UNISON
, 370
Unistat
, 339
UNITY
, 1, 45, 74, 80, 82, 83, 84, 318, 370
Universal function, 201
Universal Resource Locations (URL), 306, 308
UniVersions
database, 332
University of California, Berkeley, 337, 365
University of California, San Diego, 313
University of Sheffield, 313
Un-Scan-It
, 332
Upjohn Company, 15, 19, 22, 24, 26, 30, 42
Upperbound strategies, 50
Uracil, 147, 148, 149

Vamp
, 367
van der Waals complexes, 222
van der Waals interactions, 129
van der Waals radius, 212
van der Waals bump checking, 82
Variational method, 210
VCT90
, 90
VecBase
, 377
VectorBank
, 342
Vector-constrained 3D searches, 107
VEGAS
, 340
VEH-91
, 361
VIBMOL
, 324
VIBPLT
, 352
VIBRAM
, 324
VIBRATE
, 362
Vibrational circular dichroism (VCD), 261
Vibrational frequencies, 233, 235, 253
Vibrational transitions, 166
Vibronic coupling theory (VCT), 266, 269, 272, 279
Virial theorem, 193
Virtual databases, 109
Virtual Notebook System
, 347
Viscoelasticity
, 351
VISION3
, 324
VISTA
, 365
VOID
, 362
Volterra expansion, 189
Volume difference mapping, 94
VOWT/XMR
, 374
VSS
, 349
VSSMAC
, 324

Water, 141, 145, 146, 148, 149, 152, 153, 156, 158, 165, 166, 245, 247
Water clusters, 245, 246
Water dimer, 245, 246
Waterloo Maple Software, 343
Wavefunction functional theory, 187
Wavefunction, Inc., 313, 354
WDI93
, 368
WebCrawler, 314
Weighting schemes, 18
Westing Software, 337
WHAT IF
, 356
WHOIS, 307
Wiener index, 16
WindowChem Software, 321
WODKA
, 52, 340
Wolfrom Research, Inc., 343
World Associataion of Theoretical Organic Chemists, 316
World Wide Web, 306, 313
WPDB
, 329
WS/KOW
, 334

X-alpha approach, 234
Xenobiotic Metabolism Database
, 369
X-FIT
, 354
XMol
, 373
Xpdb
, 373
X-PLOR
, 314, 316, 353
Xsight
, 351
Xtalview
, 313, 351, 380
X-WIDGETS
, 367

Yeti
, 356

Zeneca, 40
ZINDO
, 318, 359
ZnOH-, 238

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