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Data Mining in Drug Discovery.
Written for drug developers rather than computer scientists, this monograph adopts a systematic approach to mining scientifi c data sources, covering all key steps in rational drug discovery, from compound screening to lead compound selection and personalized medicine. Clearly divided into four sect...
| Clasificación: | Libro Electrónico |
|---|---|
| Autor principal: | |
| Otros Autores: | , , , , |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
Hoboken :
Wiley,
2013.
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| Colección: | Methods and principles in medicinal chemistry.
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| Temas: | |
| Acceso en línea: | Texto completo |
Tabla de Contenidos:
- Data Mining in Drug Discovery; Contents; List of Contributors; Preface; A Personal Foreword; Part One: Data Sources; 1 Protein Structural Databases in Drug Discovery; 1.1 The Protein Data Bank: The Unique Public Archive of Protein Structures; 1.1.1 History and Background: AWealthy Resource for Structure-Based Computer-Aided Drug Design; 1.1.2 Content, Format, and Quality of Data: Pitfalls and Challenges When Using PDB Files; 1.1.2.1 The Content; 1.1.2.2 The Format; 1.1.2.3 The Quality and Uniformity of Data; 1.2 PDB-Related Databases for Exploring Ligand-Protein Recognition.
- 1.2.1 Databases in Parallel to the PDB1.2.2 Collection of Binding Affinity Data; 1.2.3 Focus on Protein-Ligand Binding Sites; 1.3 The sc-PDB, a Collection of Pharmacologically Relevant Protein-Ligand Complexes; 1.3.1 Database Setup and Content; 1.3.2 Applications to Drug Design; 1.3.2.1 Protein-Ligand Docking; 1.3.2.2 Binding Site Detection and Comparisons; 1.3.2.3 Prediction of Protein Hot Spots; 1.3.2.4 Relationships between Ligands and Their Targets; 1.3.2.5 Chemogenomic Screening for Protein-Ligand Fingerprints; 1.4 Conclusions; References.
- 2 Public Domain Databases for Medicinal Chemistry2.1 Introduction; 2.2 Databases of Small Molecule Binding and Bioactivity; 2.2.1 BindingDB; 2.2.1.1 History, Focus, and Content; 2.2.1.2 Browsing, Querying, and Downloading Capabilities; 2.2.1.3 Linking with Other Databases; 2.2.1.4 Special Tools and Data Sets; 2.2.2 ChEMBL; 2.2.2.1 History, Focus, and Content; 2.2.2.2 Browsing, Querying, and Downloading Capabilities; 2.2.2.3 Linking with Other Databases; 2.2.2.4 Special Tools and Data Sets; 2.2.3 PubChem; 2.2.3.1 History, Focus, and Content.
- 2.2.3.2 Browsing, Querying, and Downloading Capabilities2.2.3.3 Linking with Other Databases; 2.2.3.4 Special Tools and Data Sets; 2.2.4 Other Small Molecule Databases of Interest; 2.3 Trends in Medicinal Chemistry Data; 2.4 Directions; 2.4.1 Strengthening the Databases; 2.4.1.1 Coordination among Databases; 2.4.1.2 Data Quality; 2.4.1.3 Linking Journals and Databases; 2.4.2 Next-Generation Capabilities; 2.5 Summary; References; 3 Chemical Ontologies for Standardization, Knowledge Discovery, and Data Mining; 3.1 Introduction; 3.2 Background.
- 3.2.1 The OBO Foundry: Ontologies in Biology and Medicine3.2.2 Ontology Languages and Logical Expressivity; 3.2.3 Ontology Interoperability and Upper-Level Ontologies; 3.3 Chemical Ontologies; 3.4 Standardization; 3.5 Knowledge Discovery; 3.6 Data Mining; 3.7 Conclusions; References; 4 Building a Corporate Chemical Database Toward Systems Biology; 4.1 Introduction; 4.2 Setting the Scene; 4.2.1 Concept of Molecule, Substance, and Batch; 4.2.2 Challenge of Registering Diverse Data; 4.3 Dealing with Chemical Structures; 4.3.1 Chemical Cartridges; 4.3.2 Uniqueness of Records.