Chemoinformatics: A Textbook

The new discipline of chemoinformatics covers the application of computer–assisted methods to chemical problems such as information storage and retrieval, the prediction of physical, chemical or biological properties of compounds, spectra simulation, structure elucidation, reaction modeling, synthesis planning and drug design. The first work to be devoted entirely to this increasingly important field, the “Textbook” provides both an in–depth and comprehensive overview of this exciting new area. Both newcomers and advanced users as well as lecturers will find here a profound and comprehensive overview of this increasingly important field.
Edited by Johann Gasteiger and Thomas Engel (University of Erlangen–Nuremberg, Germany), the “Textbook” provides an introduction to the representation of molecular structures and reactions, data types and databases/data sources, search methods, methods for data analysis as well as such applications as structure elucidation, reaction simulation, synthesis planning and drug design. A “hands on” approach with step–by–step tutorials and detailed descrip tions of software tools and Internet resources allows easy access for beginners as well as for experienced users.
For more detailed presentation, users are referred to the “Handbook of Chemoinformatics”, which will be published separately.

Spis treści:
Foreword.
Preface.
Addresses of the Authors.
1. Introduction.
1.1. The Domain of Chemistry.
1.2. A Chemists Fundamental Questions.
1.3. The Scope of Chemoinformatics.
1.4. Learning in Chemoinformatics.
1.5. Major Tasks.
1.5.1. Representation of the Objects.
1.5.2. Data.
1.5.3. Learning.
1.6. History of Chemoinformatics.
1.6.1. Structure Databases. 10
1.6.2. Quantitative Structure––Activity Relationships.
1.6.3. Molecular Modeling.
1.6.4. Structure Elucidation.
1.6.5 . Chemical Reactions and Synthesis Design.
1.7. The Scope of this Book.
1.8. Teaching Chemoinformatics.
2. Representation of Chemical Compounds.
2.1. Introduction.
2.2. Chemical Nomenclature.
2.2.1. Development of Chemical Nomenclature.
2.2.2. Representation of Chemical Elements.
2.2.2.1. Characterization of Elements.
2.2.3. Representation of the Empirical Formulas of (Inorganic) Compounds.
2.2.3.1. Present–Day Representation.
2.2.4. Representation of the Empirical Formulas of Organic Compounds.
2.2.4.1. Present–Day Representation.
2.2.5. Systematic Nomenclature of Inorganic and Organic Compounds.
2.3. Line Notations.
2.3.1. Wiswesser Line Notation.
2.3.1.1. Applications.
2.3.2. ROSDAL.
2.3.2.1. Applications.
2.3.3. The SMILES Coding.
2.3.3.1. Applications.
2.3.4. Sybyl Line Notation.
2.3.4.1. Applications.
2.4. Coding the Constitution.
2.4.1. Graph Theory.
2.4.1.1. Basics of Graph Theory.
2.4.2. Matrix Representations.
2.4.2.1. Adjacency Matrix.
2.4.2.2. Distance Matrix.
2.4.2.3. Atom Connectivity Matrix.
2.4.2.4. Incidence Matrix.
2.4.2.5. Bond Matrix.
2.4.3. Connection Table.
2.4.4. Input and Output of Chemical Structures.
2.4.5. Standard Structure Exchange Formats.
2.4.6. Tutorial: Molfiles and SDfiles.
2.4.6.1. Structure of a Molfile.
2.4.6.2. Structure of an SDfile.
2.4.6.3. Libraries and Toolkits.
2.5. Processing Constitutional Information.
2.5.1. Ring Perception.
2.5.1.1. Minimum Number of Cycles.
2.5.1.2. All Cycles.
2.5.1.3. Smallest Fundamental Basis.
2.5.2. Unambiguous and Unique Representations.
2.5.2.1. Structure Isomers and Isomorphism.
2.5.2.2. Canonicalization.
2.5.3. The Morgan Algorithm.
2.5.3.1. Tutorial: Morgan Algorithm.
2.6. Beyond a Connection Table.
2.6.1. Deficiencies in Representing Molecular Structures by a Connection Table.
2.6.2. Representation of Molecular Structure s by Electron Systems.
2.6.2.1. General Concepts.
2.6.2.2. Simple Single and Double Bonds.
2.6.2.3. Conjugation and Aromaticity.
2.6.2.4. Orthogonality of –Systems.
2.6.2.5. Non–bonding Orbitals.
2.6.2.6. Charged Species and Radicals.
2.6.2.7. Ionized States.
2.6.2.8. Electron–Deficient Compounds.
2.6.2.9. Organometallic Compounds.
2.6.3. Generation of RAMSES from a VB Representation.
2.7. Special Notations of Chemical Structures.
2.7.1. Markush Structures.
2.7.2. Fragment Coding.
2.7.2.1. Applications.
2.7.3. Fingerprints.
2.7.3.1. Hashed Fingerprints.
2.7.4. Hash Codes.
2.7.4.1. Applications.
2.8. Representation of Stereochemistry.
2.8.1. General Concepts.
2.8.2. Representation of Configuration Isomers and Molecular Chirality.
2.8.2.1. Detection and Specification of Chirality.
2.8.3. Ordered Lists.
2.8.4. Rotational Lists.
2.8.5. Permutation Descriptors.
2.8.6. Stereochemistry in Molfile and SMILES.
2.8.6.1. Stereochemistry in the Molfile.
2.8.6.2. Stereochemistry in SMILES.
2.8.7. Tutorial: Handling of Stereochemistry by Permutation Groups.
2.8.7.1. Stereochemistry at Tetrahedral Carbon Atoms.
2.8.7.2. Stereochemistry at Double Bonds.
2.9. Representation of 3DStructures.
2.9.1. Walking through the Hierarchy of Chemical Structure Representation.
2.9.2. Representation of 3DStructures.
2.9.3. Obtaining 3DStructures and Why They are Needed.
2.9.4. Automatic 3DStructure Generation.
2.9.5. Obtaining an Ensemble of Conformations: What is Conformational Analysis?
2.9.6. Automatic Generation of Ensembles of Conformations.
2.9.7. Tutorial: 3DStructure Codes (PDB, STAR, CIF, mmCIF).
2.9.7.1. Introduction.
2.9.7.2. PDB File Format.
2.9.7.3. STAR File Format and Dictionaries.
2.9.7.4. CIF File Format (CCDC).
2.9.7.5. mmCIF File Format.
2.9.7.6. Software.
2.10. Molecular Surfaces.
2.10.1. vanderWaals Surface.
2.10.2. Connolly Surface.
2.10.3. Solvent–Accessible Surface.
2.10.4. Solvent–Excluded Surface (SES).
2.10.5. Enzyme Cavity Surface (Union Surface).
2.10.6. Isovalue–Based Electron Density Surface.
2.10.7. Experimentally Determined Surfaces.
2.11. Visualization of Molecular Models.
2.11.1. Historical Review.
2.11.2. Structure Models.
2.11.2.1. Wire Frame Model.
2.11.2.2. Capped Sticks Model.
2.11.2.3. Balls and Sticks Model.
2.11.2.4. Space–Filling Model.
2.11.3. Models of Biological Macromolecules.
2.11.3.1. Cylinder Model.
2.11.3.2. Ribbon Model.
2.11.3.3. Tube Model.
2.11.4. Crystallographic Models.
2.11.5. Visualization of Molecular Properties.
2.11.5.1. Properties Based on Isosurfaces.
2.12. Tools: Chemical Structure Drawing Software Molecule Editors and Viewers.
2.12.1. Introduction.
2.12.2. Molecule Editors.
2.12.2.1. Stand–Alone Applications.
2.12.2.2. Web–Based Applications.
2.12.3. Molecule Viewers.
2.12.3.1. Stand–Alone Applications.
2.12.3.2. Web–Based Applications.
2.13. Tools: 3DStructure Generation on the Web.
3. Representation of Chemical Reactions.
3.1. Introduction.
3.2. Reaction Types.
3.3. Reaction Center.
3.4. Chemical Reactivity.
3.4.1. Physicochemical Effects.
3.4.1.1. Charge Distribution.
3.4.1.2. Inductive Effect.
3.4.1.3. Resonance Effect.
3.4.1.4. Polarizability Effect.
3.4.1.5. Steric Effect.
3.4.1.6. Stereoelectronic Effects.
3.4.2. Simple Approaches to Quantifying Chemical Reactivity.
3.4.2.1. Frontier Molecular Orbital Theory.
3.4.2.2. Linear Free Energy Relationships (LFER).
3.4.2.3. Empirical Reactivity Equations.
3.5. Reaction Classification.
3.5.1. Model–Driven Approaches.
3.5.1.1. Hendricksons Scheme.
3.5.1.2. Ugis Scheme.
3.5.1.3. InfoChems Reaction Classification.
3.5.2. Data–Driven Approaches.
3.5.2.1. HORACE.
3.5.