Chemoinformatics: Theory, Practice, and Products Book

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