Bioinformatics: Methods and Applications: Genomics, Proteomics and Drug Discovery

Title
BioinformaticsMethods and Applications Genomics, Proteomics and Drug Discovery, FIFTH EDITION
Copyright
Dedication
CONTENTS
Preface
Preface to the First Edition
UNIT I—BIOINFORMATICS FUNDAMENTALS
1. Bioinformatics: An Introduction
	1.1 Introduction
	1.2 Historical Overview and Definition
	1.3 Molecular Biology and Bioinformatics
	1.4 Central Dogma of Molecular Biology
	1.5 Applications of Bioinformatics
	1.6 Importance of Biological Databases
	Summary
	Review Questions
2. Introduction to Biological Databases
	2.1 Introduction
	2.2 What is a Database
	2.3 Types of Databases
	2.4 Biological Databases Considerations
	2.5 Major Databases in Bioinformatics
	Summary
	Review Questions
3. Biological Database Search and Data Retrieval
	3.1 Introduction
	3.2 Tools for Web Search
	3.3 Data Retrieval Tools
	3.4 Curation, Annotation and FAIR Principles
	3.5 Data Mining of Biological Databases
	Summary
	Review Questions
UNIT II—SEQUENCE ALIGNMENT
4. Pair-wise Alignment of Sequences
	4.1 Introduction
	4.2 Biological Motivation of Alignment Problems
	4.3 Methods of Sequence Alignments
	Summary
	Review Questions
5. Scoring Matrices
	5.1 Introduction
	5.2 Building Scoring Matrices
	5.3 PAM Matrices
	5.4 BLOSUM Matrices
	5.5 PAM and BLOSUM Comparison
	Summary
	Review Questions
6. Tools for Similarity Search and Sequence Alignment
	6.1 Introduction
	6.2 Working with FASTA
	6.3 Working with BLAST
	6.4 Filtering and Gapped BLAST
	6.5 Comparison of FASTA and BLAST Algorithms
	Summary
	Review Questions
7. Alignment of Multiple Sequences
	7.1 Introduction
	7.2 Scoring MSA
	7.3 Methods of Multiple Sequence Alignment
	7.4 Evaluating Multiple Alignments
	7.5 Applications of Multiple Alignments
	Summary
	Review Questions
8. PSSMs and Hidden Markov Models
	8.1 Introduction
	8.2 Using PSSM
	8.3 Building Hidden Markov Models (HMMs
	8.4 Implementing Hidden Markov Models (HMMs
	8.5 Applications of HMMs
	8.6 Advantages and Disadvantages of HMMs
	8.7 Training HMMs
	Summary
	Review Questions
UNIT III—PHYLOGENETIC ANALYSIS
9. Introduction to Phylogenetics
	9.1 Introduction
	9.2 Taxonomic Relationships from Molecular Properties
	9.3 Terminology
	9.4 Tree Topologies
	9.5 Gene Trees
	9.6 Tools for Tree Visualization
	Summary
	Review Questions
10. Methods of Phylogenetic Analysis
	10.1 Introduction
	10.2 Distance-based Methods
	10.3 Character-based Methods
	10.4 Other Methods
	10.5 Tree Evaluation
	10.6 Problems in Phylogenetic Analysis
	10.7 Automated Tools for Phylogenetic Analysis
	Summary
	Review Questions
UNIT IV—GENOMICS
11. Gene Mapping
	11.1 Introduction
	11.2 What is a Gene
	11.3 Prokaryotic Genome
	11.4 Eukaryotic Genome
	11.5 Genome Mapping
	11.6 Genetic Linkage Mapping
	11.7 Physical Mapping
	11.8 Cloning the Entire Genome
	11.9 Applications of Genetic Maps
	11.10 The Human Genome Project (HGP
	Summary
	Review Questions
12. Gene Sequencing
	12.1 Introduction
	12.2 Genome Sequencing
	12.3 The Sequence Assembly Problem
	12.4 Sequence Assembly Tools
	12.5 Identification of Genes in Contigs
	12.6 Next-Genegration Sequence (NGS) Assembly Tools
	Summary
	Review Questions
13. Gene Prediction
	13.1 Introduction
	13.2 Biological Basis of Gene Prediction
	13.3 Pattern Recognition
	13.4 Gene Identification Using Lab Methods
	13.5 Gene Prediction Using Bioinformatics Tools
	Summary
	Review Questions
14. Regulatory Elements Prediction
	14.1 Introduction
	14.2 Transcription Regulation: An Overview
	14.3 Prediction of Regulatory Elements
	14.4 Computational Prediction Methods
	14.5 Gene Regulatory Network
	14.6 Other Gene Prediction Tools
	Summary
	Review Questions
15. Gene Expression and Microarrays
	15.1 Introduction
	15.2 Working with DNA Microarrays
	15.3 Clustering Gene Expression Profiles
	15.4 Data Sources and Tools for Microarray Analysis
	15.5 Applications of Microarray Technology
	Summary
	Review Questions
16. Comparative Genomics
	16.1 Introduction
	16.2 Comparative Genomics: The Evolutionary Context
	16.3 Principles of Comparative Genomics
	16.4 Tools for Comparative Genomics Analysis
	16.5 Limitations in Ortholog Identification
	16.6 Applications of Comparative Genomics
	Summary
	Review Questions
17. RNA Structure Prediction
	17.1 Introduction
	17.2 Secondary Structure of RNA
	17.3 Methods of RNA Structure Prediction
	17.4 Noncoding RNA (ncRNA) Prediction
	Summary
	Review Questions
UNIT V—PROTEIN STRUCTURE AND FUNCTION
18. Protein Structure Overview
	18.1 Introduction
	18.2 Overview of the Protein Structure
	18.3 Protein Structure Hierarchy
	18.4 Domain Architecture Databases
	18.5 Protein Classification Approaches
	Summary
	Review Questions
19. Protein Structure Databases: Search and Visualization
	19.1 Introduction
	19.2 Protein Structure Databases
	19.3 Comparing Protein Structures
	19.4 Protein Structure Visualization Databases and Tools
	19.5 Protein Structure Alignment
	19.6 Visualization Tools for Plotting Protein-ligand Interaction
	Summary
	Review Questions
20. Protein Structure Prediction
	20.1 Introduction
	20.2 The Protein Folding Problem
	20.3 Protein Structure Prediction Methods
	20.4 Protein Secondary Structure Prediction Methods
	20.5 Methods of Predicting Transmembrane Proteins
	20.6 Critical Assessment of Structure Prediction (CASP
	Summary
	Review Questions
21. Protein Function Prediction
	21.1 Introduction
	21.2 Overview of Protein Function Prediction
	21.3 Using Single Motif Methods
	21.4 Using Multiple Motif Methods
	21.5 Domain Alignment Methods
	21.6 Protein Function Prediction from Surface Properties
	21.7 Critical Assessment of Functional Annotation
22. Proteomics Technologies
	22.1 Introduction
	22.2 Classification of Proteomics
	22.3 Expression Proteomics
	22.4 Structural Proteomics
	22.5 Automated Tools for Proteomics
	22.6 Cell Map Proteomics
	22.7 Functional Proteomics
	22.8 Methods of Gene Family Identification
	22.9 Post-Translational Modifications (PTM
	Summary
	Review Questions
UNIT VI—DRUG DISCOVERY METHODS
23. Introduction to Drug Discovery
	23.1 Introduction
	23.2 Areas Influencing Drug Discovery
	23.3 Pharmacogenetics and Pharmacogenomics Applications
	23.4 Analysis of Single Nucleotide Polymorphisms (SNPs
	23.5 Important Parameters in Drug Discovery
	Summary
	Review Questions
24. Drug Discovery: Technologies and Strategies
	24.1 Introduction
	24.2 Drug Discovery Technologies
	24.3 Target Discovery Strategy
	24.4 Strategy to Identify Possible Drug Targets
	24.5 Target Validation
	Summary
	Review Questions
25. Cell Cycle: Key to Drug Discovery
	25.1 Introduction
	25.2 Cell Cycle at the Molecular Level
	25.3 Regulation of the Cell Cycle
	25.4 The Cell Cycle and Cancer
	25.5 Cell Cycle Target Identification and Validation
	25.6 Strategies for Identifying Inhibitors of CDKs
	Summary
	Review Questions
26. Structural Biology and Virtual Screening for Drug Discovery
	26.1 Introduction
	26.2 Target Identification Strategies
	26.3 Predicting Functionally Important Regions from Structure
	26.4 Validation and Druggability of Targets
	26.5 Virtual High-throughput in silico Screening
	Summary
	Review Questions
UNIT VII—DRUG DESIGN AND DEVELOPMENT
27. Emerging Role of Biomarkers in Drug Development
	27.1 Introduction
	27.2 Biomarker Classification
	27.3 Biomarker Discovery and Technologies
	27.4 Combinatorial Biomarkers
	27.5 Biomarkers in Drug Development
	Summary
	Review Questions
28. Potential Drug Targets
	28.1 Introduction
	28.2 Drug Identification
	28.3 Molecular Targets Overview
	28.4 Databases for Compound Identification and Interaction Prediction
	Summary
	Review Questions
29. G-Protein Coupled Receptors as Drug Targets
	29.1 Introduction
	29.2 The Family of GPCRs
	29.3 Mechanisms of Peptide Interaction with Class B GPCRs
	29.4 GPCRs as Drug Targets
	29.5 GPCR Modeling Studies
	Summary
	Review Questions
30. Ion Channels and Aquaporins as Potential Drug Targets
	30.1 Introduction
	30.2 Ion Channel Drug Discovery Needs Commercial Exploitation
	30.3 Ion Channels: Molecular Structure and Properties
	30.4 Voltage-gated Ion Channels
	30.5 Non-voltage-gated Cation Channels
	30.6 Ion Channel Drug Discovery and Technologies
	30.7 Aquaporins as Drug Targets
	30.8 Aquaporins as Targets for Drug Discovery
	Summary
	Review Questions
31. Computer-aided Drug Design
	31.1 Introduction
	31.2 Introduction to Drug Design
	31.3 Drug Design Approaches
	31.4 ADME-Tox Property Prediction
	Summary
	Review Questions
UNIT VIII—INTEGRATIVE TOPICS
32. Computational Methods for Pathways and Systems Biology
	32.1 Introduction
	32.2 Analysis of Pathways
	32.3 Metabolic Network Properties
	32.4 Metabolic Control Analysis
	32.5 Simulation of Cellular Activities
	32.6 Biological Markup Languages
	Summary
	Review Questions
Index
Back cover