Practical Protein Bioinformatics

Here is a hands-on guide to more than sixty online tools for studying proteins. Each tool is explained in practical terms, showing how to run it and how to make sense of its output, with theory kept to the minimum needed for effective use. Coverage spans three levels: protein sequences, three-dimensional structures, and the biological networks in which proteins participate.

The tools were chosen from the working experience of the authors, who run a protein bioinformatics facility at a large research centre. Every tool can be used in an ordinary web browser, so readers need no local software installation or command-line skills. The chapters address retrieving protein information, finding similar proteins, building pairwise and multiple sequence alignments, analysing domains and motifs, and reconstructing protein family phylogenies. They also cover retrieving, manipulating and visualising structures, predicting structural features and whole 3D models, mining structures for biological information, summarising large protein sets, and examining interaction and metabolic networks.

A companion website is kept current as tool addresses change and new versions appear. QR codes printed in the book link directly to each tool's site from a phone or tablet. The book is aimed at experimental researchers who need protein analysis skills but have little prior training in bioinformatics or computing.