Computational Chemogenomics

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 Jurgen Bajorath







11. SAR Matrix Method for Large-Scale Analysis of Compound Structure-Activity Relationships and Exploration of Multi-Target Activity Spaces



Ye Hu and Jurgen 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