LigAlign is a free plugin for PyMOL which implements a novel algorithm for ligand-fragment-based active site alignment. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment.
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Heifets, A., Lilien, R.,
LigAlign: Flexible ligand-based active site alignment and analysis.
Journal of Molecular Graphics and Modelling. Volume 29, Issue 1, 24 August 2010, Pages 93-101.