| | Introduction to Pharmaceutical BioinformaticsPublisher: Oakleaf Academic Publishing House. Year published: 2018,
third revised edition. ISBN 978-91-979403-1-1. 540 pages.Order book here Contents 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
Cheminformatics
Bioinformatics
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
Genotyping
Polymorphisms of drug metabolism
Polymorphisms of drug targets
Polymorphisms and adverse drug effects
Transcriptomics
Proteomics
Metabolomics
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
Conformers
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
Phylogenetics
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
Models
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
Ontologies
Domain Ontologies
The SPARQL Query Language
Linked open data
Wikidata
Limitations
Conclusion
Appendices
A. Basic probability theory
Introduction
A short history of probability theory
Some fundamental definitions
Probabilities
Random variables
Important concepts
B. Basic matrix algebra
Introduction
Matrix multiplication
Operations and properties
Index | |
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