Chemoinformatics and Computational Chemical Biology

1. Front Matter

   Pages i-x

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2. Some Trends in Chem(o)informatics

   • Wendy A. Warr

   Pages 1-37

3. Molecular Similarity Measures

   • Gerald M. Maggiora, Veerabahu Shanmugasundaram

   Pages 39-100

4. The Ups and Downs of Structure–Activity Landscapes

   • Rajarshi Guha

   Pages 101-117

5. Computational Analysis of Activity and Selectivity Cliffs

   • Lisa Peltason, Jürgen Bajorath

   Pages 119-132

6. Similarity Searching Using 2D Structural Fingerprints

   • Peter Willett

   Pages 133-158

7. Predicting the Performance of Fingerprint Similarity Searching

   • Martin Vogt, Jürgen Bajorath

   Pages 159-173

8. Bayesian Methods in Virtual Screening and Chemical Biology

   • Andreas Bender

   Pages 175-196

9. Reduced Graphs and Their Applications in Chemoinformatics

   • Kristian Birchall, Valerie J. Gillet

   Pages 197-212

10. Fragment Descriptors in Structure–Property Modeling and Virtual Screening

    • Alexandre Varnek

    Pages 213-243

11. The Scaffold Tree: An Efficient Navigation in the Scaffold Universe

    • Peter Ertl, Ansgar Schuffenhauer, Steffen Renner

    Pages 245-260

12. Pharmacophore-Based Virtual Screening

    • Dragos Horvath

    Pages 261-298

13. De Novo Drug Design

    • Markus Hartenfeller, Gisbert Schneider

    Pages 299-323

14. Classification of Chemical Reactions and Chemoinformatic Processing of Enzymatic Transformations

    • Diogo A. R. S. Latino, João Aires-de-Sousa

    Pages 325-340

15. Informatics Approach to the Rational Design of siRNA Libraries

    • Jerry O. Ebalunode, Charles Jagun, Weifan Zheng

    Pages 341-358

16. Beyond Rhodopsin: G Protein-Coupled Receptor Structure and Modeling Incorporating the β2-adrenergic and Adenosine A2A Crystal Structures

    • Andrew J. Tebben, Dora M. Schnur

    Pages 359-386

17. Methods for Combinatorial and Parallel Library Design

    • Dora M. Schnur, Brett R. Beno, Andrew J. Tebben, Cullen Cavallaro

    Pages 387-434

18. The Interweaving of Cheminformatics and HTS

    • Anne Kümmel, Christian N. Parker

    Pages 435-457

19. Computational Systems Chemical Biology

    • Tudor I. Oprea, Elebeoba E. May, Andrei Leitão, Alexander Tropsha

    Pages 459-488

20. Ligand-Based Approaches to In Silico Pharmacology

    • David Vidal, Ricard Garcia-Serna, Jordi Mestres

    Pages 489-502

Over the past years, the chem(o)informatics field has further evolved and new application areas have opened up, for example, in the broadly defined area of chemical biology. In Chemoinformatics and Computational Chemical Biology, leading investigators bring together a detailed series of reviews and methods including, among others, system-directed approaches using small molecules, the design of target-focused compound libraries, the study of molecular selectivity, and the systematic analysis of target-ligand interactions. Furthermore, the book delves into similarity methods, machine learning, probabilistic approaches, fragment-based methods, as well as topics that go beyond the current chemoinformatics spectrum, such as knowledge-based modeling of G protein-coupled receptor structures and computational design of siRNA libraries. As a volume in the highly successful Methods in Molecular Biology™ series, this collection provides detailed descriptions and implementation advice that are exceedingly relevant for basic researchers and practitioners in this highly interdisciplinary research and development area. Cutting-edge and unambiguous, Chemoinformatics and Computational Chemical Biology serves as an ideal guide for experts and newcomers alike to this vital and dynamic field of study.

• Chemical reaction modeling
• G protein-coupled receptor structures
• Molecular selectivity
• Pharmacophore concepts
• Small molecules
• Statistical standards
• Target-focused compound libraries
• Target-ligand interactions

• , Department of Life Science Informatics, Rheinische Friedrich-Wilhelms-Universitä, Bonn, Germany

  Jürgen Bajorath

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