Tutorials in Chemoinformatics (eBook, PDF)

Redaktion: Varnek, Alexandre

• Format: PDF

Produktbeschreibung

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.

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Produktdetails

• Verlag: Jossey-Bass
• Seitenzahl: 488
• Erscheinungstermin: 14. Juni 2017
• Englisch
• ISBN-13: 9781119137979
• Artikelnr.: 52560873

Autorenporträt

Edited by 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.

Inhaltsangabe

List of Contributors xv

Preface xvii

About the Companion Website xix

Part 1 Chemical Databases 1

1 Data Curation 3
Gilles Marcou and Alexandre Varnek

Theoretical

Background 3

Software 5

Step?]by?]Step Instructions 7

Conclusion 34

References 36

2 Relational Chemical Databases: Creation, Management, and Usage 37
Gilles Marcou and Alexandre Varnek

Theoretical

Background 37

Step?]by?]Step Instructions 41

Conclusion 65

References 65

3 Handling of Markush Structures 67
Timur Madzhidov, Ramil Nugmanov, and Alexandre Varnek

Theoretical Background 67

Step?]by?]Step Instructions 68

Conclusion 73

References 73

4 Processing of SMILES, InChI, and Hashed Fingerprints 75
João Montargil Aires de Sousa

Theoretical Background 75

Algorithms 76

Step?]by?]Step Instructions 78

Conclusion 80

References 81

Part 2 Library Design 83

5 Design of Diverse and Focused Compound Libraries 85
Antonio de la Vega de Leon, Eugen Lounkine, Martin Vogt, and Jürgen Bajorath

Introduction 85

Data Acquisition 86

Implementation 86

Compound Library Creation 87

Compound Library Analysis 90

Normalization of Descriptor Values 91

Visualizing Descriptor Distributions 92

Decorrelation and Dimension Reduction 94

Partitioning and Diverse Subset Calculation 95

Partitioning 95

Diverse Subset Selection 97

Combinatorial Libraries 98

Combinatorial Enumeration of Compounds 98

Retrosynthetic Approaches to Library Design 99

References 101

Part 3 Data Analysis and Visualization 103

6 Hierarchical Clustering in R 105
Martin Vogt and Jürgen Bajorath Theoretical Background 105

Algorithms 106

Instructions 107

Hierarchical Clustering Using Fingerprints 108

Hierarchical Clustering Using Descriptors 111

Visualization of the Data Sets 113

Alternative Clustering Methods 116

Conclusion 117

References 118

7 Data Visualization and Analysis Using Kohonen Self?]Organizing Maps 119
João Montargil Aires de Sousa

Theoretical Background 119

Algorithms 120

Instructions 121

Conclusion 126

References 126

Part 4 Obtaining and Validation QSAR/QSPR Models 127

8 Descriptors Generation Using the CDK Toolkit and Web Services 129
João Montargil Aires de Sousa

Theoretical Background 129

Algorithms 130

Step?]by?]Step Instructions 131

Conclusion 133

References 134

9 QSPR Models on Fragment Descriptors 135

Vitaly Solov'ev and Alexandre Varnek Abbreviations 135

DATA 136

ISIDA_QSPR Input 137

Data Split Into Training and Test Sets 139

Substructure Molecular Fragment (SMF) Descriptors 139

Regression Equations 142

Forward and Backward Stepwise Variable Selection 142

Parameters of Internal Model Validation 143

Applicability Domain (AD) of the Model 143

Storage and Retrieval Modeling Results 144

Analysis of Modeling Results 144

Root?]Mean Squared Error (RMSE) Estimation 148

Setting the Parameters 151

Analysis of n?]Fold Cross?]Validation Results 151

Loading Structure?]Data File 153

Descriptors and Fitting Equation 154