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Practical Protein Bioinformatics

Florencio Pazos & Mónica Chagoyen
Springer (2015)

This book describes more than 60 web-accessible computational tools for protein analysis. It contains detailed explanations on how to use these tools and interpret their results, and it is totally practical, with 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.

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

This is the web site associated to the book. It will keep an updated list of the tools commented in the book, reflecting changes in their web addresses, etc. In case a tool becomes unavailable, this site will reflect that and suggest alternatives.

More info on the book: [Springer] [Amazon]

Sequences

Structures

Systems