TUTORIALS IN CHEMOINFORMATICS

Part 1 Chemical Databases 1
1 Data Curation 3
2 Relational Chemical Databases: Creation, Management, and Usage 37
3 Handling of Markush Structures 67
4 Processing of SMILES, InChI, and Hashed Fingerprints 75

Part 2 Library Design 83
5 Design of Diverse and Focused Compound Libraries 85

Part 3 Data Analysis and Visualization 103
6 Hierarchical Clustering in R 105
7 Data Visualization and Analysis Using Kohonen Self ]Organizing Maps 119

Part 4 Obtaining and Validation QSAR/QSPR Models 127
8 Descriptors Generation Using the CDK Toolkit and Web Services 129
10 Cross ]Validation and the Variable Selection Bias 163
11 Classification Models 175
12 Regression Models 193
13 Benchmarking Machine ]Learning Methods 209
14 Compound Classification Using the scikit ]learn Library 223

Part 5 Ensemble Modeling 241
15 Bagging and Boosting of Classification Models 243
16 Bagging and Boosting of Regression Models 249
17 Instability of Interpretable Rules 257
18 Random Subspaces and Random Forest 263
19 Stacking 271

Part 6 3D Pharmacophore Modeling 279
20 3D Pharmacophore Modeling Techniques in Computer ]Aided Molecular Design Using LigandScout 281

Part 7 The Protein 3D ]Structures in Virtual Screening 311
21 The Protein 3D ]Structures in Virtual Screening 313

Part 8 Protein ]Ligand Docking 353
22 Protein ]Ligand Docking 355

Part 9 Pharmacophorical Profiling Using Shape Analysis 377
23 Pharmacophorical Profiling Using Shape Analysis 379

Part 10 Algorithmic Chemoinformatics 393
24 Algorithmic Chemoinformatics 395

30 tutorials and more than 100 exercises in chemoinformatics, supported by online software and data sets
Chemoinformatics is widely used in both academic and industrial chemical and biochemical research worldwide. Yet, until this unique guide, there were no books offering practical exercises in chemoinformatics methods. Tutorials in Chemoinformatics contains more than 100 exercises in 30 tutorials exploring key topics and methods in the field. It takes an applied approach to the subject with a strong emphasis on problem-solving and computational methodologies.
Each tutorial is self-contained and contains exercises for students to work through using a variety of software packages. The majority of the tutorials are divided into three sections devoted to theoretical background, algorithm description and software applications, respectively, with the latter section providing step-by-step software instructions. Throughout, three types of software tools are used: in-house programs developed by the authors, open-source programs and commercial programs which are available for free or at a modest cost to academics. The in-house software and data sets are available on a dedicated companion website.
Key topics and methods covered in Tutorials in Chemoinformatics include:
• Data curation and standardization
• Development and use of chemical databases
• Structure encoding by molecular descriptors, text strings and binary fingerprints
• The design of diverse and focused libraries
• Chemical data analysis and visualization
• Structure-property/activity modeling (QSAR/QSPR)
• Ensemble modeling approaches, including bagging, boosting, stacking and random subspaces
• 3D pharmacophores modeling and pharmacological profiling using shape analysis
• Protein-ligand docking
• Implementation of algorithms in a high-level programming language
Tutorials in Chemoinformatics is an ideal supplementary text for advanced undergraduate and graduate courses in chemoinformatics, bioinformatics, computational chemistry, computational biology, medicinal chemistry and biochemistry. It is also a valuable working resource for medicinal chemists, academic researchers and industrial chemists looking to enhance their chemoinformatics skills.

Author
Alexandre Varnek, PhD, is a professor of theoretical chemistry at The University of Strasbourg, France where he heads the Laboratory of Chemoinformatics, and is Director of two MSc programs: Chemoinformatics and In Silico Drug Design. Professor Varnek's research focuses on developing new approaches and tools for virtual screening and "in silico" design of new compounds and chemical reactions.