Practical Protein Bioinformatics

This book describes more than 60 web-accessible computational tools for protein analysis and is totally practical, with detailed explanations on how to use these tools and interpret their results and minimal mentions to their theoretical basis (only when that is required for making a better use of them). It covers a wide range of tools for dealing with different aspects of proteins, from their sequences, to their three-dimensional structures, and the biological networks they are immersed in. The selection of tools is based on the experience of the authors that lead a protein bioinformatics facility in a large research centre, with the additional constraint that the tools should be accessible through standard web browsers without requiring the local installation of specific software, command-line tools, etc.

The web tools covered include those aimed to retrieve protein information, look for similar proteins, generate pair-wise and multiple sequence alignments of protein sequences, work with protein domains and motifs, study the phylogeny of a family of proteins, retrieve, manipulate and visualize protein three-dimensional structures, predict protein structural features as well as whole three-dimensional structures, extract biological information from protein structures, summarize large protein sets, study protein interaction and metabolic networks, etc.

The book is associated to a dynamic web site that will reflect changes in the web addresses of the tools, updates of these, etc. It also contains QR codes that can be scanned with any device to direct its browser to the tool web site.

This monograph will be most valuable for researchers in experimental labs without specific knowledge on bioinformatics or computing.

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