  While many good textbooks are available on Protein Structure, Molecular
Simulations, Thermodynamics and Bioinformatics methods in general, there is no
good introductory level book for the field of Structural Bioinformatics. This
book aims to give an introduction into Structural Bioinformatics, which is
where the previous topics meet to explore three dimensional protein structures
through computational analysis. We provide an overview of existing
computational techniques, to validate, simulate, predict and analyse protein
structures. More importantly, it will aim to provide practical knowledge about
how and when to use such techniques. We will consider proteins from three major
vantage points: Protein structure quantification, Protein structure prediction,
and Protein simulation & dynamics.
  The Protein DataBank (PDB) contains a wealth of structural information. In
order to investigate the similarity between different proteins in this
database, one can compare the primary sequence through pairwise alignment and
calculate the sequence identity (or similarity) over the two sequences. This
strategy will work particularly well if the proteins you want to compare are
close homologs. However, in this chapter we will explain that a structural
comparison through structural alignment will give you much more valuable
information, that allows you to investigate similarities between proteins that
cannot be discovered by comparing the sequences alone.
