Part I: Data Resources for Computational Chemogenomics
1. A Survey of Web-Based Chemogenomic Data Resources
Rasel Al Mahmud, Rifat Ara Najnin, and Ahsan Habib Polash
2. Finding Potential Multi-Target Ligands Using PubChem
Sunghwan Kim, Benjamin A. Shoemaker, Evan E. Bolton, and Stephen H. Bryant
Part II: Fundamental Data Processing
3. Fundamental Bioinformatic and Chemoinformatic Data Processing
J.B. Brown
4. Parsing Compound-Protein Bioactivity Tables
J.B. Brown
5. Impact of Molecular Descriptors on Computational Models
Francesca Grisoni, Viviana Consonni, and Roberto Todeschini
6. Physicochemical Property Labels as Molecular Descriptors for Improved Analysis of Compound-Protein and Compound-Compound Networks
Masaaki Kotera
7. Core Statistical Methods for Chemogenomic Data
Christin Rakers
Part III: Structural Analysis Methods in 2D and 3D
8. Structure-Based Detection of Orthosteric and Allosteric Pockets at Protein-Protein Interfaces
Franck Da Silva and Didier Rognan
9. Single Binding Pockets versus Allosteric Binding
Kun Song and Jian Zhang
10. Mapping Biological Activities to Different Types of Molecular Scaffolds: Exemplary Application to Protein Kinase Inhibitors
Dilyana Dimova and Jürgen Bajorath
11. SAR Matrix Method for Large-Scale Analysis of Compound Structure-Activity Relationships and Exploration of Multi-Target Activity Spaces
Ye Hu and Jürgen Bajorath
Part IV: Statistical Pattern Recognition
12. Linear and Kernel Model Construction Methods for Predicting Drug-Target Interactions in a Chemogenomic Framework
Yoshihiro Yamanishi
13. Selection of Informative Examples in Chemogenomic Datasets
Daniel Reker and J.B. Brown
Part V: Emerging Topics
14. A Platform for Comprehensive Genomic Profiling in Human Cancers and Pharmacogenomics Therapy Selection
Tadayuki Kou, Masashi Kanai, Mayumi Kamada, Masahiko Nakatsui, Shigemi Matsumoto, Yasushi Okuno, and Manabu Muto
15. The Future of Computational Chemogenomics
Edgar Jacoby and J.B. Brown
