| Contents Notes |
1. Introduction. The Rationale for the Books ; The Objectives of Chemoinformatics ; Learning in Chemoinformatics ; Outline of the Book ; The Scope of the Book ; Teaching Chemoinformatics / Thomas Engel and Johann Gasteiger -- 2. Principles of Molecular Representations. Introduction ; Chemical Nomenclature ; Chemical Notations ; Mathematical Notations ; Specific Types of Chemical Structures ; Spatial Representation of Structures ; Molecular Surfaces / Thomas Engel -- 3. Computer Processing of Chemical Structure Information. Introduction ; Standard File Formats for Chemical Structure Information ; Input and Output of Chemical Structures ; Processing Constitutional Information ; Processing 3D Structure Information ; Visualization of Molecular Models ; Calculation of Molecular Surfaces ; Chemoinformatic Toolkits and Workflow Environments / Thomas Engel -- 4. Representation of Chemical Reactions. Introduction ; Reaction Equation ; Reaction Types ; Reaction Center and Reaction Mechanisms ; Chemical Reactivity ; Learning from Reaction Information ; Building of Reaction Databases ; Reaction Center Perception ; Reaction Classification ; Stereochemistry of Reactions ; Reaction Networks / Oliver Sacher and Johann Gasteiger -- 5. The Data. Introduction ; Data Types ; Storage and Manipulation of Data ; Conclusions -- 6. Databases and Data Sources in Chemistry. Introduction ; Chemical Literature and Databases ; Major Chemical Database Systems ; Compound Databases ; Databases with Properties of Compounds ; Reaction Databases ; Bibliographic and Citation Databases ; Full-Text Databases ; Architecture of a Structure-Searchable Database / Engelbert Zass and Thomas Engel -- 7. Searching Chemical Structures. Introduction ; Full Structure Search ; Substructure Search ; Similarity Search ; Three-Dimensional Structure Search Methods ; Sequence Searching in Protein and Nucleic Acid Databases ; Summary / Nikolay Kochev, Valentin Monev, and Ivan Bangov -- 8. Computational Chemistry. Empirical Approaches to the Calculation of Properties ; Molecular Mechanics ; Molecular Dynamics ; Quantum Mechanics / Harald Lanig, Johann Gasteiger, Tim Clark -- 9. Modeling and Prediction of Properties (QSPR/QSAR) / Johann Gasteiger -- 10. Calculation of Structure Descriptors. Introduction ; Structure Descriptors for Classification and Similarity Searching ; Structure Descriptors for Quantitative Modeling ; Descriptors That Are Not Calculated from the Chemical Structure ; Summary and Outlook / Lothar Terfloth and Johann Gasteiger -- 11. Data Analysis and Data Handling (QSPR/QSAR). Methods for Multivariate Data Analysis ; Artificial Neural Networks (ANNs) ; Deep and Shallow Neural Networks / Kurt Varmuza, Jure Zupan, David A. Winkler -- 12. QSAR/QSPR Revisited. Best Practices of QSAR Modeling ; The Data Science of QSAR Modeling / Alexander Golbraikh and Alexander Tropsha -- 13. Bioinformatics. Introduction ; Sequence Databases ; Searching Sequence Databases ; Characterization of Protein Families ; Homology Modeling / Heinrich Sticht -- 14. Future Directions. Access to Chemical Information ; Representation of Chemical Compounds ; Representation of Chemical Reactions ; Learning from Chemical Information ; Training in Chemoinformatics / Johann Gasteiger. This guide to the knowledge and tools in the field includes the basic concepts and modern methods, while also forming a bridge to bioinformatics. The textbook starting from the basics and the theory, before going on to provide an overview of the methods. Exercises are included at the end of each section or chapter. Software tools are explained in detail, so that the students not only learn the necessary theoretical background, but also how to use the different software packages available. |
