Textbook of Chemoinformatics - Contents
- Introduction
- Representation of Chemical Compounds
- Representation of Chemical Reactions
- The Data
- Databases/Datasources
- Databases/Datasources
- Calculation of Physical and Chemical Data
- Calculation of Structure Descriptors
- Methods for Data Analysis
- Applications
1. Introduction
- The Domain of Chemistry
- A Chemist's Fundamental Questions
- The Scope of Chemoinformatics
- Learning in Chemoinformatics
- Major Tasks
- History of Chemoinformatics
- The Scope of this Book
- Teaching Chemoinformatics
2. Representation of Chemical Compounds
- Introduction
- Chemical Nomenclature
- Linear Notations
- TUTORIAL: SMILES coding
- Coding the Constitution
- TUTORIAL: Molfile, SDfile etc.
- Processing of Constitutional Information
- TUTORIAL: Morgan Algorithm
- Inadequacies of representing molecular structures in a connection table
- Special Notations
- Representation of Stereochemistry
- TUTORIAL: Handling of Stereochemistry by Permutation Groups
- Representation of 3D Structures
- TUTORIAL: 3D Structure Codes (PDB, CCDC)
- Molecular Surfaces
- Visualization of Molecular Models
- TOOLS: Molecule Editors and Viewer
- TOOLS: 3D Structure Generation (on the web)
3. Representation of Chemical Reactions
- Introduction
- Reaction Types
- Reaction Center
- Chemical Reactivity
- Reaction Classification
- Stereochemistry of Reactions
- TUTORIAL: Stereochemistry of Reactions
- Conclusions and Outlook
4. The Data
- Introduction
- Data Acquisition
- Data Pre-processing
- Preparation of data sets for the validations of the qualities of models
- Concluding remarks
5. Databases/Datasources
- Introduction
- Types of Database Systems
- Classification of Databases
- Literature Databases
- TUTORIAL: Using the Chemical Abstracts System
- Physical Properties Databases
- TUTORIAL: Searching in the Beilstein Database
- Spectroscopic Databases
- Crystallographic Databases
- Molecular Biological Databases
- Structure Databases
- Reaction Databases
- TUTORIAL: Searching in the ChemInform Reaction Database
- Patent Databases
- Chemical Information on the Internet
- TUTORIAL: Searching the Internet for Chemical Information
- TUTORIAL: Searching Environmental Information in the Internet
- TOOLS: The Internet (Online DB in Chemistry)
6. Structure Search Methods
- Introduction
- Complete Structure Search
- Substructure Search
- Similarity Search
7. Calculation of Physical and Chemical Data
- Empirical Approaches to the Calculation of Properties
- Molecular Mechanics
- Molecular Dynamics
- Quantum Mechanics
8. Calculation of Structure Descriptors
- Introduction
- Structure keys and 1D fingerprints
- Topological descriptors
- 3D descriptors
- Chirality descriptors
- TUTORIAL: Conformation-independent and conformation-dependent chirality codes
- Further descriptors
- Non-structure-based descriptors
- Properties of structure descriptors
9. Methods for Data Analysis
- Inductive Learning Methods
- Machine Learning Techniques
- Decision trees
- Chemometrics
- TUTORIAL: eDAS
- Neural Networks
- Fuzzy Sets and Fuzzy Logic
- Genetic Algorithms
- Data Mining
- Expert Systems
10. Applications
- Prediction of Properties of Compounds
- TUTORIAL: Structure Spectra Correlations
- TOOLS: TeleSpec: Simulation of Infrared Spectra
- TOOLS: Simulation of 1H NMR
- Chemical Reactions and Synthesis Design
- The Prediction of Chemical Reactions
- TUTORIAL: Prediction of regiochemistry in pyrazole synthesis
- Computer-Assisted Synthesis Design
- TUTORIAL: Using the WODCA System
- Drug Design