Basic Chemoinformatics: Textbook, A

Description:
This 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. Edited by Johann Gasteiger and Thomas Engel, the book 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 descriptions of software tools and Internet resources allows easy access for newcomers, advanced users and lecturers alike. For a more detailed presentation, users are referred to the 'Handbook of Chemoinformatics', which will be published separately. Johann Gasteiger is the recipient of the 1991 Gmelin-Beilstein Medal of the German Chemical Society for Achievements in Computer Chemistry, and the Herman Skolnik Award of the Division of Chemical Information of the American Chemical Society (ACS) in 1997. Thomas Engel joined the research group headed by Johann Gasteiger at the University of Erlangen-Nuremberg and is a specialist in chemoinformatics.

Review:
'The Handbook of Chemoinformatics is the first reference work to be exclusively devoted to this developing field from data to knowledge, and will set the standard as the premier information source for the next decade. This handbook is a must read for experts as well as students of chemistry and biology...rich in content...should find a place in every chemoinformaticians desk and every university library in the world...' M. Karthikeyan of the Digital Information Resource Center, National Chemical Laboratory, Pune, India www.review.molecularsociety.org, 18 June 2004 '...certainly fills an empty niche...well written...the referencing and provided links are an excellent resource...' (Journal of Chemoetrics, Vol.18, No.6 June 2004) '...certainly fills an empty niche...well written...the referencing and provided links are an excellent resource...' Journal of Chemoetrics, Vol.18, No.6 June 2004

Table of Contents:
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. 101.6.2. 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 Structures 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.3.5.2.2. Reaction Landscapes.3.6. Stereochemistry of Reactions.3.7. Tutorial: Stereochemistry of Reactions.4. The Data.4.1. Introduction.4.1.1. Data, Information, Knowledge.4.1.2. The Data Acquisition Pathway.4.2. Data Acquisition. 2064.2.1. Why Does the Quality of Data Matter?4.2.2. Data Complexity.4.2.3. Experimental Data.4.2.4. Data Exchange.4.2.4.1. DAT files.4.2.4.2. JCAMP-DX.4.2.4.3. PMML.4.2.5. Real-World Data and their Potential Drawbacks.4.3. Data Pre-processing.4.3.1. Mean-Centering, Scaling, and Autoscaling.4.3.2. Advanced Methods.4.3.2.1. Fast Fourier Transformation.4.3.2.2. Wavelet Transformation.4.3.2.3. Singular Value Decomposition.4.3.3. Variable Selection.4.3.3.1. Genetic Algorithm (GA)-Based Solutions.4.3.3.2. Orthogonalization-Based Solutions.4.3.3.3. Simulated Annealing (SA)-Based Solutions.4.3.3.4. PCA-Based Solutions.4.3.4. Object Selection.4.4. Preparation of Datasets for Validation of the Model Quality.4.4.1. Training and Test Datasets.4.4.2. Compilation of Test Sets.5. Databases and Data Sources in Chemistry.5.1. Introduction.5.2. Basic Database Theory.5.2.1. Databases in the Information System.5.2.2. Search Engine.5.2.3. Access to Databases.5.2.4. Types of Database Systems.5.2.4.1. Hierarchical Database System.5.2.4.2. Network Model.5.2.4.3. Relational Model.5.2.4.4. Object-Based Model.5.3. Classification of Databases.5.3.1. Literature Databases.5.3.2. Factual Databases.5.3.2.1. Numeric Databases.5.3.2.2. Catalogs of Chemical Compounds.5.3.2.3. Research Project Databases.5.3.2.4. Metadatabases.5.3.3. Structure Databases.5.3.4. Reaction Databases.5.4. Literature Databases.5.4.1. Chemical Abstracts File.5.4.2. SCISEARCH.5.4.3. Medline (Medical Literature, Analysis, and Retrieval System Online).5.5. Tutorial: Using the Chemical Abstracts System.5.5.1. Online Access.5.5.2. Access to CAS with SciFinder Scholar 2002.5.5.2.1. Getting Started.5.5.2.2. Searching within Various Topics.5.6. Property (Numeric) Databases.5.6.1. Beilstein Database.5.6.2. Gmelin.5.6.3. DETHERM.5.7. Tutorial: Searching in the Beilstein Database