Handbook - Contents

Contents

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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

Chapter (Author)

1. The Scope of Chemoinformatics (Gasteiger, J.)
2. A History of Chemoinformatics (Willett, P.)

II. Representation of Chemical Compounds

1. Representation of Molecular Structures - Overview (Barnard, J.)
2. Nomenclature: Automatic Generation and Conversion (Wisniewski, J. L.)
3. SMILES - A language for Molecules and Reactions (Weininger, D.)
4. Graph Theory in Chemistry (Ivanciuc, O.)
5. Processing Constitutional Information

5.1 Canonical Numbering and Constitutional Symmetry (Ivanciuc, O.)
5.2 Ring Perception (Downs, G.Y)
5.3 Topological Structure Generators (Bangov, I.)
5.4 Combinatorics of Organic Molecular Structures (Weininger, D.)

6. Representation and Manipulation of Stereochemistry (Rohde, B.)
7. Representation of 3D Structures

7.1 3D Structure Generation (Sadowski, J.)
7.2 Conformational Analysis and Searching (Schwab, C.)

8. Molecular Shape Analysis (Polanski, J.)
9. Computer Visualization of Molecular Models –
Tools for Man–MachineCommunication in Molecular Science (Brickmann, J.)

III. Representation of Chemical Reactions

3.1 Reaction Classification and Knowledge Acquisition (Chen, L.)

IV. The Data

1. Data Types (Tomczak, J.)
2. Data Acquisition

2.1 Quality Control and Data Analysis (Booth, D.)
2.2 Experimental Design (Marsili, M.)

3. Standard Exchange Formats for Spectral Data (Davies, A.)
4. XML and its Application in Chemistry (Rzepa, H., Murray-Rust, P.)

V. Databases/Data Sources

1. Overview of Databases/Data Sources (Wiggins, G.)
2. Bibliographic Databases (Barth, A.S.)
3. Databases of Chemical Structures (Paris, G. C.)
4. The CAS Information System: Applying Scientific Knowledge and Technology for Better Information (Fisanick, W.; Shively, E. R.)
5. The Beilstein Database (Lawson, A. J.)
6. Databases in Inorganic Chemistry (Vogt, J.; Vogt, N.; Schunk, A.)
7. The Cambridge Structural Database (CSD) of Small Molecule Crystal Structures (Allen, F.; Lipscomb, K.J.; B. Gary)
8. Databases on Chemical Reactions (Zass, E.)
9. Spectroscopic Databases (Davies, A.N.; Neudert, R.)
10. Databases on Environmental Information (Voigt, K.)
11. Patent Databases (Vogt, J.)
12. Databases in Biochemistry and Molecular Biology (von Homeyer, A.; Reitz. M.)
13. Chemistry on the Internet (Tarkhov, A.)
14. Laboratory Information Management Systems (LIMS) (Hemmer, M.)

VI. Structure Search Methods

1. 2D-Structure and Substructure Searching (Xu, J.)
2. Current State of the Art of Markush Topological Search Systems (Berks, A.H.)
3. Similarity Searching in Chemical Structure Databases (Willett, P.)

VII. Calculation of Physical and Chemical Data

1. Molecular Mechanics (Lanig, H.)
2. Quantum Mechanics (Clark, T.)

VIII. Descriptors for Chemical Compounds

1. Topological Indices (Ivanciuc, O.)
2. Descriptors from Molecular Geometry (Todeschini, R.; Consonni, V.)
3. A Hierarchy of Structure Representations (Gasteiger, J.)
4. Representation of Molecular Chirality (Aires de Sousa, J.)

IX. Methods for Data Analysis

1. Inductive Learning Methods

1.1 Machine Learning Techniques in Chemistry (Rose, J. R.)
1.2 Multivariate Data Analysis in Chemistry (Varmuza, K.)
1.3 Partial Least Squares (PLS) in Chemoinformatics (Eriksson, L.; Antti, H.; Holmes, E.; Johansson, E.; Lundstedt, T.; Svante, W.)
1.4 Neural Networks (Zupan, J.)
1.5 Fuzzy Set Theory and Fuzzy Logic and its Application to Molecular Recognition (Exner, T.E.; Keil, M.; Brickmann, J.)
1.6 Evolutionary Algorithms and Applications in Chemistry (von Homeyer, A.)

2. Expert Systems (Hemmer, M.)

X. Applications

1. Prediction of Physical and Chemical Properties

1.1 Octanol/Water Partition Coefficients (Mannhold, R.)
1.2 Quantitative Structure-Property Relationships (Jurs, P. C.)
1.3 Web-based Calculation of Molecular Properties (Ertl, P. Selzer, P.)

2. Structure-Spectra Correlations

2.1 Correlations between Chemical Structure and Infrared Spectra (Selzer, P.)
2.2 Correlations between Chemical Structure and NMR Data (Steinbeck, C.)
2.3 Computer-Assisted Structure Elucidation (Steinbeck, C.)

3. Chemical Reactions and Synthesis Design

3.1 Analysis of Reaction Information (Grethe, G.)
3.2 Computer-Assisted Synthesis Design (CASD) (Barone, R.; Chanon, M.)
3.3 Computer-Assisted Synthesis Design (CASD) (Pförtner, M.; Sitzmann, M.)

4. Drug Design

4.1 Chemoinformatics and the Quest for Leads in Drug Discovery (Oprea, T.I.)
4.2 QSAR in Drug Design (Kubinyi, H.)
4.3 Comparative Molecular Field Analysis (CoMFA) (Kubinyi, H.)
4.4 3D- and nD-QSAR Methods (Esposito, E.X.; Hopfinger, A.J.; Madura, J.D.)
4.5 High-Throughput Chemistry (Warr, W.A.)
4.6 Molecular Diversity (Farnum, M.A; DesJarlais, R.L.; Agrafiotis, D.)
4.7 Pharmacophore and Drug Discovery (Nicklaus, M.C.)
4.8 de novo Design Systems (Johnson, P. A.)
4.9 The Docking Problem (Sotriffer, C.; Stahl, M.; Klebe, G.)
4.10 From Structural Genomics to Drug Design: Knowledge Discovery in Crystallographic Databases to Assist Lead Discovery and Optimization (Klebe, G.)

5. Chemoinformatics/Bioinformatics

5.1 Prediction of Protein Structure Through Evolution (Rost, B.; Liu, J.; Przybylski, D.; Nair, R.; Wrzeszczynski, K.O.; Bigelow, H.; Ofran, Y.)
5.2 Sequence and Genome Bioinformatics (Mewes, H.-W.)

XI. Future Directions (Gasteiger, J.)

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