Practical Protein Bioinformatics

INTRODUCTION
1. SEQUENCES
- INTRODUCTION
- REPRESENTING PROTEIN SEQUENCES IN THE COMPUTER Sequence file formats
Sequence format conversion tools
MAIN PROTEIN SEQUENCE DATABASES
BASIC SEQUENCE-BASED CHARACTERISTICS
COMPARE TWO PROTEIN SEQUENCES
Types of pair-wise sequence alignments
FINDING SIMILAR SEQUENCES IN A DATABASE (BASIC)
Which sequence database to search?
BLAST
COMPARE MORE THAN TWO SEQUENCES
Multiple Sequence Alignments: Formats and Conversion
Alignment editing and representation
Summarizing MSAs
FINDING SIMILAR SEQUENCES IN A DATABASE (ADVANCED) Sequence profiles
Iterative profile construction
HMM profile search against a sequence database
HMM profile search against a profile database
PROTEIN MOTIFS, DOMAINS AND FAMILIES
BASIC PHYLOGENY
2. STRUCTURES
INTRODUCTION
Storing protein structures - The PDB file format
MAIN PROTEIN STRUCTURE DATABASES
Classifications of structural domains
STRUCTURE MANIPULATION, VISUALIZATION AND COMPARISON
Structure Manipulation and Visualization
Structure Comparison
PREDICTION OF 1D STRUCTURAL FEATURES
Secondary structure and solvent accessibility
Transmembrane segments
Coiled-coils
Disordered regions
Protein sorting signals
PREDICTING PROTEIN 3D STRUCTURE
Template-based (homology-based approaches)
Template-based (fragment-based approaches)
Model quality checks
ANALYSIS OF PROTEIN STRUCTURE
Mapping conservation
Protein and ligand contacts
Surface clefts, binding pockets, tunnels and internal cavities
3. SYSTEMS
INTRODUCTION
Protein/gene functional annotations
ID conversions
ANNOTATION ENRICHMENT ANALYSIS OF LARGE PROTEINS SETS
PROTEIN INTERACTION NETWORKS
METABOLIC NETWORKS
Retrieve the metabolic-related information associated to a protein of interest
Map a large set of proteins in the metabolome
OTHER BIOLOGICAL NETWORKS
BIBLIOGRAPHY
HOW TO
TOOLS INDEX