About the Structure alignment algorithm
The structure alignment algorithm contained in BioJava is based on a
variation of the PSC++ algorithm provided by Peter Lackner, Univ.
Salzburg (personal communication). The algorithm is calculating a
distance matrix based, rigid body protein structure superimposition. See
also a JavaWebStart example of how it works at
What can it do?
calculate alignments of
* whole structures,
* single chains
* any set of atoms
* it provides alternative solutions
* alternative solutions are clustered to groups of similar alignments
How does it work?
* It identifies short fragments in two protein structures that have similar intra-molecular distances.
* The pairs of fragments are then compared and if possible, joined to longer fragments.
* Finally the fragments are undergoing a refinement procedure in order to extend them to full size alignments.