Introduction to Pharmaceutical Bioinformatics

Publisher: Oakleaf Academic Publishing House. Year published: 2018,
third revised edition. ISBN 978-91-979403-1-1. 540 pages.

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           1. Introduction

           2. Background

                     Drugs and their origins
                     The modern pharmaceutical industry
                     Sciences dealing with drugs
                     Molecular basis of drug actions
                     The drug in the living organism
                     Open and closed source software

           3. Drug discovery and development
                     The drug discovery phase
                     Clinical trials
                     Cheminformatics and molecular modeling
                     Open source software for drug design

           4. Bioinformatics, drugs and omics
                     Genome sequencing
                     Polymorphisms of drug metabolism
                     Polymorphisms of drug targets
                     Polymorphisms and adverse drug effects

           5. Representing molecules
                     Chemical graph
                     Connection matrices
                     Connection tables
                     Line notation systems
                     File formats
                     Substructure and query representation

           6. Representation of 3D structures
                     Coordinate systems
                     Geometry optimization
                     Comparing geometries

           7. Molecular descriptors
                     Vectorial representations
                     Molecular descriptors
                     Structural keys
                     Molecular fingerprints
                     Grid approaches
                     Information content

           8. Sequence analysis
                     Introduction to sequence analysis
                     Representation of sequences
                     Sequence alignments
                     Next-Generation Sequencing

           9. Macromolecular descriptors
                     Building blocks
                     Alignment-based descriptions
                     Alignment-independent approaches
                     3D based methods

           10. Design of experiments
                     Principles of experimental design
                     Step-by-step design of experiments
                     Common experimental designs
                     Statistical molecular design

           11. Data analysis
                     Introduction to data analysis
                     Nomenclature and notation
                     Supervised learning
                     Unsupervised learning

           12. Databases
                     Introduction to databases
                     Nucleotide databases
                     Protein databases
                     Chemistry databases
                     Interaction databases
                     Pathway databases
                     Drug target databases
                     Bibliographic databases
                     Data integration

           13. QSAR
                     Activities studied in QSAR and QSPR
                     History of QSAR
                     QSAR today
                     QSAR in industry and society
                     Future perspective for QSAR

           14. Proteochemometrics
                     Introduction to proteochemometrics
                     Cross-terms in proteochemometrics
                     The interaction space
                     Statistical validation of PCM models
                     Proof of concept for PCM
                     Examples of PCM use
                     Current status of PCM
                     Future prospectives for PCM

           15. Semantic web
                     Open Semantic Web Standards
                     File formats
                     Domain Ontologies
                     The SPARQL Query Language
                     Linked open data


           A. Basic probability theory
                     A short history of probability theory
                     Some fundamental definitions
                     Random variables
                     Important concepts

           B. Basic matrix algebra
                     Matrix multiplication
                     Operations and properties

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