LigAlign

The ligalign function provides access to a rigid and flexible ligand alignment algorithm, created by Abraham Heifets, and Ryan H. Lilien, that offers solid alignment performance with a few more features.

Here's the abstract from the reference:

Ligand-based active site alignment is a widely adopted technique for the structural analysis
of protein–ligand complexes. However, existing tools for ligand alignment treat the ligands
as rigid objects even though most biological ligands are flexible. We present LigAlign, an 
automated system for flexible ligand alignment and analysis. 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.

ligalign command, pivot_object, target_object(s) [, options ]

Valid commands are:

• rigid, for rigid ligand alignment
• flexible, for flexible ligand alignment

Valid options for the given commands are:

• for command=rigid
  • pivot_object
  • target_object(s)
• for command=flexible
  • pivot_object
  • target_object(s)
• for command=template
  • radius
  • similarity
  • fraction
• for command=color
  • selection
• for command=reset
• for command=set
  • argument
• for command=cite

• LigAlign Home Page
• Reference
• In PyMOL, to find the citation information for LigAlign, please type, “ligalign cite”.