  Aligning multiple protein structures can yield valuable information about
structural similarities among related proteins, as well as provide insight into
evolutionary relationships between proteins in a family. We have developed an
algorithm (msTALI) for aligning multiple protein structures using biochemical
and biophysical properties, including torsion angles, secondary structure,
hydrophobicity, and surface accessibility. The algorithm is a progressive
alignment algorithm motivated by popular techniques from multiple sequence
alignment. It has demonstrated success in aligning the major structural regions
of a set of proteins from the s/r kinase family. The algorithm was also
successful at aligning functional residues of these proteins. In addition, the
algorithm was also successful in aligning seven members of the acyl carrier
protein family, including both experimentally derived as well as
computationally modeled structures.
