EFI - Enzyme Similarity Tool

This web resource is supported by a Research Resource from the National Institute of General Medical Sciences (R24GM141196-01).
The tools are available without charge or license to both academic and commercial users.
Important Notice

The UniProtKB database used by the EFI tools is undergoing major reorganization starting with the 2025_04 release (https://www.uniprot.org/release-notes/forthcoming-changes). When the reorganization is fully implemented (2026_02 release, Spring 2026), the number of proteins in UniProtKB is expected to decrease from ~253M accessions in the current 2025_03 release to ~141M accessions in the 2026_02 release.

In response to these changes, we are planning to provide the current 2025_03 release until the 2026_02 release is available.

More information about the changes is located here.

EFI-EST and Cytoscape Tutorials

References

1.Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC (2009) PLoS One 4, e4345.

2. Pythoscape: a framework for generation of large protein similarity networks. Barber AE 2nd, Babbitt PC (2012) Bioinformatics 28, 2845-6.

3. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Genome Res 13, 2498-504.

4. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Weizhong L, Godzik A (2006) Bioinformatics 22, 1658-9. 

5. CD-HIT: accelerated for clustering the next generation sequencing data. Fu L, Niu B, Zhu Z, Wu S, Li W (2012) Bioinformatics 28, 3150-2.

6. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL. (2015) Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics doi:10.1016/j.bbapap.2015.04.015

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