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?

View the source code

* 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.

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