Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks
By J. Gerlt, J. Bouvier, D. B. Davidson, Heidi J. Imker, Boris Sadkhin, David R. Slater, Katie Whalen. Biochimica et Biophysica Acta, 2015
739 citations recorded by the source corpus.
The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their “favorite” protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the “closest neighbors” of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/7c47c5160981a8df4548319ed0afe5531ae5cab8
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Citations in the corpus
- Chemical transformation of xenobiotics by the human gut microbiota (2017, methodology): “Collaborative efforts such as the Enzyme Function Initiative have advanced bioinformatic and experimental approaches for functionally characterizing such enzymes (123), including protein sequence similarity and genome neighborhood network analyses, high-throughput ligand docking, and structural geno”
- antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification (2017, methodology): “For example, antiSMASH predictions are also available through the Joint Genome Institute’s IMG-ABC (33) as well as Genoscope’s framework MicroScope (34); connections to EFI-EST (35) and other tools are being investigated.”
- A new genome-mining tool redefines the lasso peptide biosynthetic landscape (2016, methodology): “SSNs were generated using EFI-EST (http://efi.igb.illinois.edu/efi-est/) 27 .”