Table of Contents

Preface

1. Blueprint of life

Gene and genome
DNA and protein
Central dogma
RNA world
Cell
Technological developments in molecular biology
Human Genome Project
Reductionism in biology
Grand challenges in post-genome informatics
Genetic and chemical blueprints of life

2. Molecular biology databases

2-1. Historical background

Evolution of molecular biology databases
Bibliographic database
Amino acid sequence database
Three-dimensional structure database
Nucleotide sequence database
Flat file format
Genome databases

2-2. Informatics technologies

Relational database
Deductive database
Object-oriented database
Link-based integration
Knowledge base
World Wide Web
Computer graphics

2-3. New generation of molecular biology databases

Elements and compounds
Amino acid indices
Protein families and sequence motifs
Classification of protein 3D structures
Orthologues and paralogues
Reactions and interactions
Biochemical pathways
Genome diversity

3. Sequence analysis of nucleic acids and proteins

3-1. Similarity search

Problems in sequence analysis
Dynamic programming
Global alignment
Local alignment
Database search
FASTA algorithm
BLAST algorithm
Statistical significance
Multiple alignment
Phylogenetic analysis
Simulated annealing
Genetic algorithms

3-2. Prediction of structures and functions

Thermodynamic principle
Prediction of RNA secondary structures
Hopfield neural network
Prediction of protein secondary structures
Prediction of transmembrane segments
Hierarchical neural network
Hidden Markov model
Formal grammar
Prediction of protein 3D structures
Gene finding and functional predictions
Expert system for protein sorting prediction

4. Network analysis of molecular interactions

4-1. Network representation and computation

Level of abstraction
Molecular networks
Graph
Common subgraph
Heuristic network comparison
Path computation
Binary relation and deduction
Implementation

4-2. Principles of biochemical networks

Metabolic network
Genomic perspective
Protein-protein interaction network
Gene regulatory network
Network principles
Complex systems

Appendix. Methods in computational molecular biology - Bibliography