A comprehensive overview of bioinformatics and computational biology techniques applied to proteins. Multiple chapters discuss protein evolution, including methods for ancestral sequence reconstruction (ASR) and the use of phylogenetic models to understand gene duplication and coevolution. Significant focus is placed on protein structure prediction and modeling, detailing techniques such as homology modeling using tools like SWISS-MODEL and the structural alignment method StructAlign. Furthermore, the text introduces software and protocols for analyzing amino acid mutations (e.g., ELASPIC and methods for calculating free energy changes) and for running high-throughput molecular dynamics simulations to assist in enzyme engineering using frameworks like CADEE.
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