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Textbook - Contents

Learning Objectives

Essentials

Interesting Websites

Tutorials

 

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Textbook Comments
1. Introduction
2. Representation of Chemical Compounds
3. Representation of Chemical Reactions
4. The Data
5. Databases/Datasources
6. Structure Search Methods
7. Calculation of Physical and Chemical Data
8. Calculation of Structure Descriptors
9. Methods for Data Analysis
10. Applications

  • 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

11. Future Directions

12. Appendices

A1: Software Development

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Markus Sitzmann
Thomas Engel 2003
Contact: Thomas Engel
last update: 2003-10-19