Number sequence representation of protein structures based on the second   derivative of a folded tetrahedron sequence
  This paper proposes a new mathematical approach to characterize native protein structures based on the discrete differential geometry of tetrahedron tiles. In the approach, local structure of proteins is classified into finite types according to shape. And one would obtain a number sequence representation of protein structures automatically. As a result, it would become possible to quantify structural preference of amino-acids objectively. And one could use the wide variety of sequence alignment programs to study protein structures since the number sequence has no internal structure.   The programs and this paper with clear figures are available from http://www.genocript.com. 
Naoto Morikawa