Practical Protein Bioinformatics

Abstract

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