Similarity ensemble approach (SEA)

The Similarity ensemble approach relates proteins based on the set-wise chemical similarity among their ligands. It can be used to rapidly search large compound databases and to build cross-target similarity maps.

How to use SEA

You can try SEA yourself via the online SEA search tool.

SEA is a collaborative project provided by the Keiser Laboratory in the Institute for Neutrodegenerative Diseases and the Irwin and Shoichet laboratories in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
Caveat Emptor! SEA is provided free-of-charge in the hope that it will be useful, but you must use it at your own risk. We make no guarantees about data confidentiality on this public service website. If you would like to use SEA securely, please contact John Irwin at chemistry4biology at

To determine whether SEA's predictions for your compounds are already known, we recommend you visit the extensive Ki Database at the NIMH Psychoactive Drug Screening Program.

How to cite SEA

If you use SEA results in your publications, please cite the following:

Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007).
Pubmed | DOI | PDF

The following SEA results were referenced in this paper:

Database   Results
MDL Drug Data Report    Similarity map1
Similarity map2
Significance scores (raw data)

1 AT&T Graphviz
2 Cytoscape

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