eMatchSite Webserver

eMatchSite is a sequence order-independent algorithm for ligand binding site alignment and matching. It accurately identifies pairs of pockets that bind similar compounds even in proteins with different global structures.
If you use eMatchSite, please cite the following papers:

eMatchSite is also available as a standalone software distribution. Datasets are available for download from here. See the manual for the details on the output file format.

eMatchSite is free of charge under the terms of GNU General Public License for the general public and under a dual license for commercial users.

This server is running eMatchSite v1.0. Click here to see some sample results.


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3-10 alphanumerical characters.


Provide eFindSite ticket for the first protein.


Provide eFindSite ticket for the second protein.


eFindSite pocket number (first protein).


eFindSite pocket number (second protein).


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© Michal Brylinski
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