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eMatchSite

 
 
standalone
 

A sequence order-independent algorithm to align and match ligand binding sites. eMatchSite accurately identifies those pockets binding similar compounds even in proteins with different global structures. Furthermore, it tolerates, to a large extent, structural distortions in protein models, thus experimentally solved structures are not required.

  
eMatchSite
If you use eMatchSite, please cite the following papers:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.