Enzyme Function Initiative - Enzyme Similarity Tool

EFI-EST is a flexible pipeline which builds Sequence Similarity Networks of proteins for the purpose of elucidating the function of enzymes. It is available through a web tool at https://efi.igb.illinois.edu/efi-est/ and on KBase. This respository contains the analysis code that these services use.

Running the Pipelines

Please see our documentation for comprehensive information on using the pipelines.

Contributors

The EFI tools were originally created by Daniel Davidson ([email protected]), and further developed by David Slater ([email protected]), Hunter DeMeyer ([email protected]), and Nils Oberg ([email protected]). Additional contributors were Rémi Zallot, Katie Whalen, Heidi Imker, and Boris Sadkhin. John Gerlt ([email protected]) envisioned the project and provided continual oversight and feedback.

Copyright and License Information

The EFI tools are copyright 2012-2024 University of Illinois and are licensed under the GPL v3 license (see LICENSE).

Third-party tools are used in the pipelines but are not included in the EFI source code repository, and therefore do not fall under the license and copyright of this project.

Citing

Please cite your use of EFI-EST.

Rémi Zallot, Nils Oberg, and John A. Gerlt, The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019 58 (41), 4169-4182. https://doi.org/10.1021/acs.biochem.9b00735

Nils Oberg, Rémi Zallot, and John A. Gerlt, EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. J Mol Biol 2023. https://doi.org/10.1016/j.jmb.2023.168018

Papers

1. Nils Oberg, Rémi Zallot, and John A. Gerlt, EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. J Mol Biol 2023. https://doi.org/10.1016/j.jmb.2023.168018

2. Rémi Zallot, Nils Oberg, and John A. Gerlt, The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019 58 (41), 4169-4182. https://doi.org/10.1021/acs.biochem.9b00735

3. Rémi Zallot, Nils Oberg, John A. Gerlt, "Democratized" genomic enzymology web tools for functional assignment, Current Opinion in Chemical Biology, Volume 47, 2018, Pages 77-85, https://doi.org/10.1016/j.cbpa.2018.09.009

4. John A. Gerlt, Genomic enzymology: Web tools for leveraging protein family sequence–function space and genome context to discover novel functions, Biochemistry. Volume 56, 2017, Pages 4293-4308. https://doi.org/10.1021/acs.biochem.7b00614

5. John A. Gerlt, Jason T. Bouvier, Daniel B. Davidson, Heidi J. Imker, Boris Sadkhin, David R. Slater, Katie L. Whalen, Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1854, Issue 8, 2015, Pages 1019-1037, ISSN 1570-9639, https://dx.doi.org/10.1016/j.bbapap.2015.04.015