Tutorials in Chemoinformatics E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 681

Veröffentlichungsjahr: 2017

Beschreibung

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.

Leseprobe

Tutorials in Chemoinformatics

Edited by Alexandre Varnek

University of Strasbourg, Strasbourg, France

This edition first published 2017© 2017 John Wiley & Sons Ltd

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The right of Alexandre Varnek to be identified as the author of this editorial material in this work has been asserted in accordance with law.

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Library of Congress Cataloging‐in‐Publication data applied for

ISBN: 9781119137962

Cover image: (molecules) © alice‐photo/Gettyimages; (computers) © loops7/iStockphotoCover design by Wiley

List of Contributors

João Montargil Aires de SousaLAQV‐REQUIMTE and Departamento de QuimicaUniversidade Nova de Lisboa Portugal

Jürgen BajorathDepartment of Life Science Informatics Rheinische Friedrich‐Wilhelms‐Universität BonnBonnGermany

Jenny BalferDepartment of Life Science InformaticsRheinische Friedrich‐Wilhelms‐Universität BonnBonnGermany

Igor I. BaskinDepartment of PhysicsLomonosov Moscow State UniversityMoscowRussia

Guillaume BretMedalis Drug Discovery CenterUniversity of StrasbourgIllkirchFrance

Sharon D. BryantInteLigand GmbHViennaAustria

Antonio de la Vega de LeonDepartment of Life Science InformaticsRheinische Friedrich‐Wilhelms‐Universität BonnBonnGermany

Jérémy DesaphyMedalis Drug Discovery CenterUniversity of StrasbourgIllkirchFrance

Dragos HorvathLaboratory of Chemoinformatics (UMR 7140 CNRS/UniStra)University of StrasbourgStrasbourgFrance

Gökhan IbisInteLigand GmbHViennaAustria

Esther KellenbergerMedalis Drug Discovery CenterUniversity of StrasbourgIllkirchFrance

Thierry LangerUniversity of Vienna, Department of Pharmaceutical ChemistryViennaAustria

Eugen LounkineNovartis Institutes for Biomedical Research In Silico Lead DiscoveryCambridge, MassachusettsUSA

Timur MadzhidovInstitute of ChemistryKazan Federal UniversityKazanRussia

Gilles MarcouLaboratory of Chemoinformatics (UMR 7140 CNRS/UniStra)University of StrasbourgStrasbourgFrance

Ramil NugmanovInstitute of ChemistryKazan Federal UniversityKazanRussia

Giulio PoliDepartment of PharmacyUniversity of PisaPisaItaly

Didier RognanMedalis Drug Discovery CenterUniversity of StrasbourgIllkirchFrance

Thomas SeidelUniversity of Vienna, Department ofPharmaceutical ChemistryViennaAustria

Inna SlynkoMedalis Drug Discovery CenterUniversity of StrasbourgIllkirchFrance

Vitaly Solov’evA.N. Frumkin Institute of Physical Chemistry and Electrochemistry RASMoscowRussia

Alexandre VarnekLaboratory of Chemoinformatics (UMR 7140 CNRS/UniStra)University of StrasbourgStrasbourgFrance

Martin VogtDepartment of Life Science InformaticsRheinische Friedrich‐Wilhelms‐Universitat BonnBonnGermany

Preface

Chemoinformatics methods are widely used both in academic research and in industrial applications. They represent an important part of curricula of numerous chemistry and pharmacology MSc and PhD programs running practically in all European countries, in United States, Australia, Japan, Korea, and Canada. Since early 2000, several dozens of books devoted to various applications of chemoinformatics have been published. Surprisingly, among them, there were very few textbooks.[1–3] To our knowledge, no books describing practical exercises in chemoinformatics have been published so far. Here, we fill this gap by presenting 30 tutorials assembling more than 100 exercises developed either for the master programs running at the University of Strasbourg (France), Rheinische Friedrich‐Wilhelms University of Bonn (Germany), New University of Lisbon (Portugal), University of Vienna (Austria), Lomonosov Moscow State University (Russia), and Kazan Federal University (Russia), or for five international Strasbourg Summer Schools in Chemoinformatics (CS3) in the period 2008–2016. These tutorials cover all main areas in chemoinformatics: chemical databases, library design, chemical data analysis, structure—property/activity modeling, pharmacophore modeling, and docking. Each tutorial contains a short theoretical part, algorithm description (if necessary), and software instructions.

The book is divided into 10 parts devoted to different applications of chemoinformatics. Part 1 is devoted to chemical databases with four tutorials related to data curation and standardization, creation of a local database, manipulations with the Markush structures, and structure encoding by text and bit strings. Part 2 concerns design of focused and diverse compounds libraries, whereas Part 3 describes data visualization and analysis using hierarchical clustering and self‐organizing maps. Parts 4 and 5 are devoted to structure‐property/activity models (QSAR/QSPR). Beginners should start with the exercises in Part 4