Dr. Thomas Engel - Faculty for Chemistry and Pharmacy
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Textbook of Chemoinformatics
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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
11. Future Directions
12. Appendices
A1: Software Development