Perspectives in Drug Discovery and Design, 20: 289, 2000. KLUWER/ESCOM Author Index Volume 20 2000 Bradshaw,J., 1 Knegtel,R.M.A., 191 Rose,P.W., 209 Briem, H., 231 Kostka, T., 245 Kuhn, L.A., 171 Sadowski, J., 17 Caflisch, A., 145 Sacher, O., 245 Lemmen, C., 43 Scarsi, M., 145 Davies, T.G., 29 Lengauer, T., 43,63 Schnecke, V., 171 Lessel, U.f., 231 Sitzmann, M., 245 Gasteiger, J., 245 Luty, B.A., 209 Stahl,M., 83 Gillet, V.J., 265 Ginn, C.M.R., 1 Majeux, N., 145 Tame, J.R.H., 29 Gohlke, H., 115 Marrone, T.J., 209 Tenette-Souaille, C., 145 Mestres, J., 191 Hendlich, M., 115 Muegge,I., 99 Willett, P., 1 Höllering, R., 245 Hubbard, R.E., 29 Nicolotti, O. 265 Zimmermann, M., 43 Karg,N., 245 Pförtner, M., 245 Klebe, G., 115 Rarey,M., 63
Perspectives in Drug Discovery and Design, 20: 291 295, 2000. KLUWER/ESCOM Subject Index Volume 20 2000 2D base placement 47 descriptors 233,242 beta adrenergic blockers 12 fingerprint 6,204 binding similarity 5, 56, 83, 233 3D-QSAR 193 affinities 34, 38, 73, 93, 113, 116, 125, 232 analysis 46 energy 165 3D free energy 225 database searches 232 mode 99, 145 descriptors 232, 242 site fingerprint 6,12 characteristics 172 pharmacophore 83 solvation 177, 187 similarity 56, 201, 204 waters 178 methods 196 bioactivity profiles 265 5-HT3 antagonist 236 bit-string 5, 8 buried water 42 accessibility 86, 89 ACD 197 Cambridge Crystallographic Database ACE inhibitor 236 180 acetylcholine receptor inhibitors 12 Cambridge structural database 141 active analogue approach 44 chemical ADME properties 192, 232 database 5 affinity 29 diversity 199 fingerprints, 231 reactions 246, 257 AGDOCK 2 16 reactivity 246, 250, 252, 254 aldose reductase inhibitors 12 clique detection 45 anchor fragment 176 angiotensin cliques 51 clustering 175 -converting enzyme inhibitor 12 procedure 153 -II receptor antagonists 12 similar molecules 64 aqueous buffers 36 co-crystallisation 37 arabinose-binding protein 136 combinatorial argatroban 36 chemistry v, vii, 17, 191, 204, 245, assays 30 26 1, 262, 265 atom pair potentials 100 docking 63, 69, 71, 116 Available Chemicals Directory 19, 273 library 24, 63 47, 204, 246, 273, 285
292 library design 265, 281 compatibility graph 45 screening 187 geometry 44 computational docking 210 graph 51 computing times 77 diversity 17, 27, 245, 265, 266, 274 conformation 44 measure 278 conformational DOCK 65, 83, 120, 164, 194, 234, 235 analysis 63 docking vii, 64, 83, 116, 171, 186, 194, change 31 232 entropy 228 methods 196 searching 64, 172, 186 dopamine 3 receptor (ant)agonists 12 space 220 drug consensus scoring 95 design 63, 145 conserve 178 discovery 36 continuum drug-like 245, 266, 270, 281, 285 electrostatics 155, 164 molecules vii, 22 1, 234 solvation 153 drug-likeness 17-19 CORINA 180,197 DrugScore 117,140 Coulomb field 149 COX2 84 electrostatic crop protection score 22 desolvation 145, 148 cross-over 24 interactions 156, 227 crystal structure 128 potential 195 crystallographic data 52 empirical cyclo oxygenase 212 energy function 217 knowledge 116 data free energy function 210 fusion 1 2, 12 scoring potential 38 mining 267 endothelin receptor (ant)agonists, 12 database endothermic process 33 screening 173, 191 endothiapepsins 129 searching 1,231 enrichment 53, 55, 238 Daylight fingerprints 12 13, 54, 55, 237, factors 87 90 274,275,282 EROS system 250,256,261,263 de novo design 146,164 enthalpy 34,39 descriptor vi, 5, 266, 274 -entropy relationship 229 -based methods 46 entropic effect 147 matching 173 entropy 34,39,40 design 30 exothermic binding 33 desolvation 155, 157, 216, 227 DHFR 71, 84, 92 farnesyltransferase 164 dielectric constant 148,156 FBSS 11 dihydrofolate reductase 180, 182 feature trees 237 directional hydrophobic interactions 48 fingerprints 6, 17 25, 232, 233 directionality 118, 121 fitness 24 distance FKBP 214
293 flexibility 40, 171 hydrophilic zone 146 flexible superpositioning 49 hydrophobic FlexS 46 fragments 159 FLEXX 65 67, 79, 83 84, 92, 95, 118, interaction 174 120,235 regions 164 Fourier space 47 zone 146 fragment bit-strings 1 hydrophobicity 145, 146, 179 fragment libraries 165 incremental construction 47, 173 Gaussian interaction centers 175 functions 47 interactions 30 representations 51, 55 intermolecular hydrogen bonding 173 genetic algorithms 17 26, 234, 268, 278 internal rotations 228 genome projects 165 ISOSTAR 134 geometric hashing 45 isothermal titration calorimetry 31 GOLD 83,120 GRASP 149 kinetic data 31 knowledge based 116, 140 H-bonding geometries 48 potentials 117 hashing approach 175 scoring function 91, 99, 100, 113, heat of dilution 34 127,242 Helmholtz free Kohonen networks 245 energy 99 interaction energies 117 L-arabinose binding proteins 129 hierarchical data structures 68 large database 171 high-throughput lead optimization 192 data 20 library screening v, 17, 191, 196, 204, 209, design 65, 191, 245, 273, 283 231,232,245,265 screening 209 histamine 2 antagonists 12 ligand hit binding 29 discovery 192 conformation 40 optimization 192 docking 145 -to-lead 232 linkers 212 HIV-protease 84 Lipinsky s rule vii HIV-1 protease 12, 157 LUDI 38, 65, 227 HMG-CoA reductase inhibitor 236 Hodgkin index 47 MAP kinase 152 hot spots 138, 141 MCSS 65 HQSAR 237 MDDR 236 human genome v medicinal chemistry 30 hydrogen bond 83, 85, 89 metalloproteases 129 acceptor 174 MIMIC 195 donor 174 mitogen-activated protein (MAP) kinase geometries 153 150
294 molecular ligand-binding modes 118 descriptors 193, 204, 231, 285 product docking 63,242 -based selection 265 holograms 237 level 273 recognition 145 similarity 1, 43, 193, 231 progesterone receptor 180 protein-bound water 178 surface 149, 157 Protein Data Bank 203 multiple copy simultaneous search 164 protein-ligand binding 99 flexible superposition 59 mutation 24 complexes 29, 38, 52, 150, 225 interactions 30, 116, 192 protonation states 140 NAPAP 150,197 -thrombin complex 162 PteusScore 132 NCI 58, 180 neural networks 17 19, 256, 257, 258, QSAR 5, 13, 231 model 233 271 neurokinase- 1 receptor 12 reactant NMR 209 -based selection 265 level 273 one-body potential 119 reaction OppA 36 classification 245 prediction 245 P38 MAP 164 PAF antagonist 236 receptor -fragment complex 157 pair -potentials 118 ligand interaction 63 reference preferences 140 alignment 52 PDB protein-ligand complexes 129 penicillin acylase 30 state 99, 102, 113 relative orientation 44 perturbation 116 ReLiBase 119 PETRA 247, 248 RigFit 46 pharmacophore -based search 180 root-mean-square deviation (rmsd) 124 rotamer libraries 173, 186 modelling vi pharmacophoric groups 45 Rule-of-five Lipinski 266 physicochemical SAR by NMR 91 descriptors 258 SCORE1 132 properties 193, 266, 267, 281, 285 scoring 83, 178 PMFScore 132 functions 41, 84 91, 95, 99, 112, 116, PMF scoring 99 positions of polar hydrogen atoms 140 117, 164, 172, 187, 204, 224 screening 171 potential of mean force 117,118 predict binding affinities 118, 129 SEED 146 serine proteases 129 shape-complementary 176
295 sialidase 36 signalling cascades 152 synthesis design 245 similarity vi, 194, 232, 247, 257, 278 Tanimoto coefficient 1, 6, 275 measure 1 6, 11,45, 195 targeted libraries vi score 3, 6, 196 Theilheimer database 261 search 2, 5, 11 15 thermodynamics 29, 30, 229 singlet preference 123, 140 integration 116 SMoGScore 132 thermolysin 134, 136 soaking 37 thrombin 71, 73, 84, 88, 92, 134, 150, so!vation 112, 173 159,197 models 146 -NAPAP 164 properties vii thymidylate synthase 84 solvent trypsin 134 accessible regions 214 accessible surface 119 effects 155 TXA2 236 UNITY fingerprints 11, 274, 275, 280 -mediated effects 119 specific recognition 29 uracil-dna glycosylase 180, 181 SPRESI 268, 270, 275 vibrational freedom 40 statistical preferences 121 steric-volume field 195 strain energy term 228 strategic bonds 245, 248 virtual stromelysin 221 structural diversity 273 191, 231, 232 structure-based water 75, 150 database screening 45, 51 NMR screening 210, 224 screening v, vi, 83, 95, 99, 116, 124, approaches 201 -mediated design 64 hydrogen bonds 178 ligand design 146, 172 interactions 172, 173 substructure searches 245, 248 structure 147 superposition vii WODCA 246, 248, 263 superpositioning of molecules 43 World Drug Index (WDI) 11, 19, 85-87, Superstar 138, 139 268, 270, 281 Sybyl 197