Practical Protein Bioinformatics - Chagoyen, Mónica

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Résumé :
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.

Sommaire:

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 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