When performing site-directed mutagenesis experiments to study protein structure-function relationships, ideally one would know the structure of the protein under study. It is also very useful to have structures of multiple related proteins in order to determine whether or not particular amino acid residues are conserved in the structures either in the active site of an enzyme at the surface of a protein or at a putative protein-protein interface. While many protein structures are available in the Protein Data Base (PDB), a structure of the protein of interest may not be available. In the study of reversible and often transient protein-protein interactions it is rare to have a structure of the complex of the two interacting proteins. In this chapter, methods are described for comparing protein structures, generating putative structures of proteins with homology models based on the protein primary sequence, and generating docking models to predict interaction sites between proteins and cofactor-protein interactions. The rationale used to predict mutagenesis targets from these structures and models is also described.
Keywords: Homology model; Ligand docking; Protein Data Bank (PDB); Protein docking; Structural alignment.