Computational Chemogenomics

Front Matter ....Pages i-xii
Front Matter ....Pages 1-1
 A Survey of Web-Based Chemogenomic Data Resources  (Rasel Al Mahmud, Rifat Ara Najnin, Ahsan Habib Polash)....Pages 3-62
 Finding Potential Multitarget Ligands Using PubChem  (Sunghwan Kim, Benjamin A. Shoemaker, Evan E. Bolton, Stephen H. Bryant)....Pages 63-91
Front Matter ....Pages 93-93
 Fundamental Bioinformatic and Chemoinformatic Data Processing  (J. B. Brown)....Pages 95-129
 Parsing Compound–Protein Bioactivity Tables  (J. B. Brown)....Pages 131-170
 Impact of Molecular Descriptors on Computational Models  (Francesca Grisoni, Viviana Consonni, Roberto Todeschini)....Pages 171-209
 Physicochemical Property Labels as Molecular Descriptors for Improved Analysis of Compound–Protein and Compound–Compound Networks  (Masaaki Kotera)....Pages 211-225
 Core Statistical Methods for Chemogenomic Data  (Christin Rakers)....Pages 227-277
Front Matter ....Pages 279-279
 Structure-Based Detection of Orthosteric and Allosteric Pockets at Protein–Protein Interfaces  (Franck Da Silva, Didier Rognan)....Pages 281-294
 Single Binding Pockets Versus Allosteric Binding  (Kun Song, Jian Zhang)....Pages 295-326
 Mapping Biological Activities to Different Types of Molecular Scaffolds: Exemplary Application to Protein Kinase Inhibitors  (Dilyana Dimova, Jürgen Bajorath)....Pages 327-337
 SAR Matrix Method for Large-Scale Analysis of Compound Structure–Activity Relationships and Exploration of Multitarget Activity Spaces  (Ye Hu, Jürgen Bajorath)....Pages 339-352
Front Matter ....Pages 353-353
 Linear and Kernel Model Construction Methods for Predicting Drug–Target Interactions in a Chemogenomic Framework  (Yoshihiro Yamanishi)....Pages 355-368
 Selection of Informative Examples in Chemogenomic Datasets  (Daniel Reker, J. B. Brown)....Pages 369-410
Front Matter ....Pages 411-411
 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 et al.)....Pages 413-424
 The Future of Computational Chemogenomics  (Edgar Jacoby, J. B. Brown)....Pages 425-450
Back Matter ....Pages 451-454