  The Automated Protein Structure Analysis (APSA) method, which describes the
protein backbone as a smooth line in 3-dimensional space and characterizes it
by curvature kappa and torsion tau as a function of arc length s, was applied
on 77 proteins to determine all secondary structural units via specific
kappa(s) and tau(s) patterns. A total of 533 alpha-helices and 644 beta-strands
were recognized by APSA, whereas DSSP gives 536 and 651 units, respectively.
Kinks and distortions were quantified and the boundaries (entry and exit) of
secondary structures were classified. Similarity between proteins can be easily
quantified using APSA, as was demonstrated for the roll architecture of
proteins ubiquitin and spinach ferridoxin. A twenty-by-twenty comparison of
all-alpha domains showed that the curvature-torsion patterns generated by APSA
provide an accurate and meaningful similarity measurement for secondary,
super-secondary, and tertiary protein structure. APSA is shown to accurately
reflect the conformation of the backbone effectively reducing 3-dimensional
structure information to 2-dimensional representations that are easy to
interpret and understand.
