Index
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Y
Z
Index
A
- accessing the combinatorial chemistry modules, 113
- adjacency matrix, 248
- A-matrix, 247
- Analog Builder control panel, 129, 136
- Analog Builder Preferences control panel, 176
- analog structures
- reusing R-groups, 129
- save fragments in an SD file, 136
- analysis of descriptor correlation, 169
- analysis of property distribution, 166
- array design, 229
- augmentation of libraries, 215
B
- Balaban indices, 243
- BDB file, 155
- BDF files, 175
- bdf files, 176
- and dep files, 179
- creating, 176
- plotting data, 180
- selecting rows from, 180
- using, 177
- BDF Preferences control panel, 175, 179
- BDF Selection plot, 181
- bdf_rows file, 180
- Bin Analysis control panel, 172, 173
- bin file, 172
- Binary Data File control panel, 175, 180
- binary data file system, 99
- binary data files, 175
- binning, 170
- binning criteria, 170
- binning table, 171
- Binning Thresholds control panel, 171
- Building combinatorial libraries, 19
C
- candidate library, 220, 221, 223
- cell-based comparison, 218
- Cell-Based Selection control panel, 174
- cell-based selections, 196
- cluster analysis, 188
- cluster-based selections, 193
- clustering methods, 188
- combinatorial design, 229
- Compare Libraries Cell Based control panel, 218
- Compare Libraries Cosine Coeff Diversity control panel, 220
- Compare Libraries 3D Fingerprints Onbits control panel, 221
- Comparison (library), 166
- computer memory, conserving, 174, 176
- convergence (in stochastic optimization), 263
- cosine-coefficient diversity metric, 220, 255
- cosine-coefficient similarity metric, 220
D
- Data, 255
- data files, 19
- Data mining techniques, 166
- datafiles, 177
- data-reduction techniques, 255
- Daylight descriptors, 146
- Daylight fingerprints, 153
- Daylight installation/setup, 14
- Define Binning control panel, 170, 171
- demonstration files, 19
- dependent parameters and derivations, 179
- descriptor
- correlation, 169
- descriptor space, 183
- descriptors, 235
- adding to study table, 147
- Calculation, 147
- calculation, fast, 151
- Catalyst type, 142
- choice, 139
- Daylight, 146
- definitions, 235
- electronic, 235
- E-state, 146
- fast calculation, 151
- field (3D), 140
- fingerprints, 140
- geometric, 235
- information content, 249
- information-theoretic, 246, 249
- loading, 149
- managing, 149
- partial charges, 253
- preferences, 153
- properties, 139
- redefined sets, 153
- redundant, 169
- spatial, 235
- standard sets, 139
- Surface area, 251
- surface area, 235
- thermodynamic, 235
- distance histograms, 224
- distance matrix, 259
- distance-based selections, 195
- diverse library, 230
- diverse subsets, 193
- diversity functions, 260
- definition, 260
- selection, 195
- diversity visualization, 183
- diversity vs. Monte Carlo step, 263
- D-matrix, 248
- D-optimal design, 260
E
- edge adjacency matricies, 249
- ED-matrix, 249
- eigenvalues, 259
- eigenvectors, 259
- E-matrix, 249
- Euler formula, 243
- Export BDF data to Study Table control panel, 175
F
- factor analysis, 147
- Fast Descriptors control panel, 152
- feature file, 155
- file based system, 175
- files
- bdf, 153
- fingerprints
- modal, 221
- 2D, 221, 255
- 3D, 221, 223
- fingerprints OnBits metric, 221
- Fix Fragments control panel, 230
- focused libraries, 231
- focused library, 230
- fragment selection, 22
G
- graph theory (descriptors), 236
- graph-theoretic, 236
- Green, M., 218
H
- Hall valence-modified connectivity, 243
- histogram labels, 173
- histogram of molecular property space, 170
- histograms, 221
- Holes in libraries, 222
- Hosoya index, 237
I
- IAC index, 247
- IAC-mean, 247
- IAC-total, 247
- independent groups (variables), 149
- Information matrix, 233
- Installation (Cerius2), 13
- intermolecular distances, 259
- Isis keys, 153
- ISIS setup, 16
K
- Kier and Hall E-state, 146
- Kier & Hall subgraph count index, 237
- Kier &, 243
- Kier's alpha-modified shape indices, 243
- Kier's shape indices, 237
L
- large libraries, 99, 174
- Lead discovery, 114
- LibEngine, 147
- Library characterization, 123
- Library comparison, 218
- library comparison, 215
- library subsetting, 193
- Load Fast Descriptors Set control panel, 153
M
- MaxMin diversity function, 260
- MDS (multidimensional scaling), 259
- mean pairwise intermolecular dissimilarity, 255
- merging files, 177
- metric functions, 260
- metric matrix, 259
- metric space definitions, 234
- metropolis criterion, 263
- minimal p, 237
- molecular flexibility index, 243
- molecular structures, recovering, 177, 180
- Molecular surface, 251
- Monte Carlo algorithm, 263
- multigraph indices, 249
N
- normalization factors, 180
O
- Oracle import, 121
- Oracle setup, 16
- outlier identification, 193
P
- partial charges, 253
- PCA, 184, 233
- PCA descriptor plot, 184
- Pearlman, R. S., 218
- pharmacophores
- catalyst query, 164
- displaying, 158
- planning diversity experiments, 114
- powerSum diversity function, 260
- principal component analysis, 113
- Principal Component Analysis (PCA), 184
- probability distribution, 236
- product diversity function, 260
- property distribution, 166
- property profiles, 205
- property ranges, 204
R
- random, 199
- random selections, 199
- reagent penalty restraints, 207, 212
- penalty function, 211
- reagent table, 209
- supplier table, 209
- suppliers table, 211
- reagents penalty function, 211, 265
- reference library, 220, 221, 223
- relocation clustering, 194
- representative subsets of compounds, 170
- reproducibility, 195
- restrained library, 230
- RG file import/export, 120
- Rgroup subsetting Diverse Library control panel, 220
- Rgroup subsetting optimization, 230
S
- samples plot, 183
- Save Fast Descriptors Set control panel, 153
- scaffold (or core) structure, 19
- screening libraries, 230
- SD file import, 24, 152
- SD File Preferences control panel, 176
- seed molecules, 194
- Select Fast Descriptors control panel, 153
- Select SD file for Fast Descriptors control panel, 152
- Select SMILES file for Fast Descriptors control panel, 152
- selecting similar compounds, 198
- Shadow indices, 251
- shape index, 237
- similar compounds (selecting), 198
- SMILES, 148
- Smiles import/export, 117, 152
- starting diversity, 113
- stochastic optimization, 263
- storing and retrieving libraries, 23
- subgraph, 236
T
- termination criteria, 263
- topological, 236
- Turner, D. B., 255
- typographical conventions, 11
- Tyrrel, S. M., 255
V
- Variance, 233
- vertex (adjacency/distance/equality/magnitude/valence), 237
- vertices, 236
- visualization (library), 183
W
- Wang, X. C., 218
- Wiener index, 237
- Willett, P. J., 255
X
- Xu, Y., 218
Z
- Zagreb index, 237
- zero-iteration relocation clustering, 194
Numerics
- 2D Fingerprints Daylight control panel, 153
- 2D Fingerprints ISIS keys control panel, 153
- 3D fingerprint file, 156
- 3D Pharmacaphore fingerprints, 154
- 3D Plot Samples control panel, 180
- 3DKeys, 154
- BDB file, 155
- feature file, 155
- 3PF, 4PF files, 156
- 3Dplot from BDF control panel, 175
Last updated May 19, 2000 at 01:54PM Pacific Daylight Time.
Copyright © 2000, Molecular Simulations Inc. All rights
reserved.