| Foreword | p. ix |
| Chemoinformatics Theory | p. 1 |
| Chemoinformatics - What is it? | p. 1 |
| Chemo-versus Bio-informatics | p. 2 |
| Scientific Origins | p. 4 |
| Fundamental Concepts | p. 4 |
| Molecular descriptors and chemical spaces | p. 4 |
| Chemical spaces and molecular similarity | p. 7 |
| Molecular similarity, dissimilarity, and diversity | p. 8 |
| Modification and simplification of chemical spaces | p. 9 |
| Compound Classification and Selection | p. 11 |
| Cluster analysis | p. 12 |
| Partitioning | p. 13 |
| Support vector machines | p. 16 |
| Similarity Searching | p. 17 |
| Structural queries and graphs | p. 17 |
| Pharmacophores | p. 18 |
| Fingerprints | p. 21 |
| Machine Learning Methods | p. 23 |
| Genetic algorithms | p. 23 |
| Neural networks | p. 24 |
| Library Design | p. 26 |
| Diverse libraries | p. 27 |
| Diversity estimation | p. 28 |
| Multi-objective design | p. 29 |
| Focused libraries | p. 29 |
| Quantitative Structure-Activity Relationship Analysis | p. 31 |
| Model building | p. 31 |
| Model evaluation | p. 32 |
| 3D-QSAR | p. 33 |
| 4D-QSAR | p. 34 |
| Probabilistic methods | p. 35 |
| Virtual Screening and Compound Filtering | p. 35 |
| Biologically active compounds | p. 35 |
| Virtual and high-throughput screening | p. 36 |
| Filter functions | p. 38 |
| From Theory to Practice | p. 40 |
| Database design | p. 40 |
| Compound selection for medicinal chemistry | p. 42 |
| Computational hit identification | p. 45 |
| References | p. 47 |
| Practice and Products | p. 51 |
| Accelrys | p. 51 |
| ACD Labs | p. 59 |
| Barnard Chemical Information Ltd | p. 67 |
| BioByte | p. 69 |
| Cambridge Soft | p. 73 |
| CAS/Scifinder | p. 80 |
| ChemAxon | p. 87 |
| Chemical Computing Group | p. 98 |
| ChemInnovation Software | p. 103 |
| ChemNavigator | p. 109 |
| Chimera-Dock-Zinc from UCSF | p. 112 |
| Collaborative Drug Discovery (CDD, Inc.) | p. 115 |
| Daylight | p. 123 |
| Eidogen-Sertanty (previously Libraria) | p. 127 |
| Fujitsu Biosciences Group (previously Cache) | p. 137 |
| Genego | p. 140 |
| GVK-Bio | p. 144 |
| Hypercube | p. 148 |
| IDBS | p. 152 |
| Infochem | p. 156 |
| Jubilant Biosys | p. 164 |
| Leadscope | p. 169 |
| MDL | p. 171 |
| Milano Chemometrics and QSAR Research Group | p. 180 |
| Molecular Discovery | p. 184 |
| Molecular Networks | p. 187 |
| Open Eye Scientific Software | p. 194 |
| Planaria-Software | p. 202 |
| PubChem | p. 203 |
| PyMol | p. 208 |
| RasMol and Protein Explorer | p. 211 |
| Schrodinger, LLC | p. 215 |
| Scinova Technologies | p. 223 |
| Scitegic | p. 226 |
| Simulation Plus, Inc. | p. 229 |
| Spotfire | p. 236 |
| Summit PK | p. 239 |
| Symyx | p. 243 |
| TimTec | p. 254 |
| Tripos | p. 259 |
| Subject Appendices | |
| Drug Discovery Informatics Registration Systems and Underlying Toolkits (Appendices 1 and 2) | |
| Drug, Molecular Registration Systems, and Chemistry Data Cartridges | p. 271 |
| Chemoinformatics Toolkits to Develop Applications | p. 272 |
| Content Databases (Appendices 3-7) | |
| Compound Availability Databases | p. 273 |
| SAR Database | p. 273 |
| Chemical Reaction Databases | p. 274 |
| Patent Databases | p. 275 |
| Other Compound and Drug Databases | p. 275 |
| Drug, Molecule, and Protein Visualization (Appendices 8-10) | |
| Chemical Drawing, Structure Viewing and Modeling Packages | p. 276 |
| Data Analysis and Mining Tools | p. 276 |
| Small Molecule - Protein Visualization Tools | p. 277 |
| Modeling and Algorithms (Appendices 11-17) | |
| Molecular Descriptors | p. 278 |
| Clogp, Tpsa, and Lipinski Property Calculation Systems | p. 279 |
| Qsar/Pharmacophore Programs | p. 279 |
| Docking and Crystallographic Software | p. 280 |
| Quantum Mechanics Calculations | p. 280 |
| PK/ADME/Tox Databases and Predictors | p. 280 |
| Multi-parameter Drug Development/Identification Software | p. 281 |
| Index | p. 283 |
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