ABSTRACT
This chapter discusses the concepts behind structure comparison methods and describes some example methods, and representative of different philosophical approaches. It considers some of the challenges faced when comparing protein structures. Automatic structure comparison methods were introduced in the 1970s shortly after the first crystal structures were deposited in the protein structure databank (PDB). Protein structure is much more highly conserved than sequence during evolution. Thus protein structure comparison can be used to detect similarity between homologous proteins whose sequences have changed substantially during evolution. Approaches for comparing protein structures generally fall into the following categories: methods which superpose protein structures and measure intermolecular distances; and methods which compare intramolecular distances or vectors. Although the PDB is currently much smaller than the sequence databases by nearly three orders of magnitude, the international structural genomics initiatives will help to populate the database and provide representative structures for many protein families.
