ReviewBiochimica et biophysica acta2015
Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
Review in Biochimica et biophysica acta, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 472 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
472 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The diversity of PET degrading enzymes: A systematic review of sequence, structure, and function.Protein science : a publication of the Protein Society · 2025Pooled it
- Graph-based representations in modern protein science.The Biochemical journal · 2026Review
- Synthesis of Six Natural Products Enabled by Selective Hydroxylation of Orcinaldehyde-Like Substrates With an Enzyme Library.Angewandte Chemie (International ed. in English) · 2026Article
- Discovery and characterization of a nickel enzyme family that catalyses intermolecular hydride shuttling.Nature chemistry · 2026Article
- Article
- Iterative acylation on mature lasso peptides by widespread acetyltransferases.Nature chemical biology · 2026Article
- The microbiome regulates host metabolic health and diseases through microbial enzymes.Nature reviews. Gastroenterology & hepatology · 2026Review
- Structural evolution of a fungal cell wall protein family for β-glucan-binding and cell separation.mBio · 2026Article
- The structure of the SufBCbioRxiv : the preprint server for biology · 2026Article
- The Factors Governing Metal Dependence of an Emergent Superfamily of Bimetallic Oxygenases.Journal of the American Chemical Society · 2026Article
- AI-Assisted Isolation of Bioactive Dipyrimicins fromJournal of natural products · 2026Article
- A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome.bioRxiv : the preprint server for biology · 2026Article
- A single viral enzyme drives tRNA-dependent hypermodification of DNA at adenine.Nature communications · 2026Article
- A Pangenome Framework Reveals Conserved Pathogenicity-Associated Biosynthetic Gene Clusters in Fusarium equiseti, a Root Rot Pathogen of Panax notoginseng.Molecular plant pathology · 2026Article
- Bacterial Siderophore Production in Metal-Rich Environments: Underexplored Sources of Siderophores and Insights into Bioremediation.Journal of natural products · 2026Review
- Novel chemistry and structural perspectives in vitamin BChemical science · 2026Review
- Discovery and engineering of bacterial P450s for C-14 hydroxylation in ent-kaurane diterpenoids.Nature communications · 2026Article
- PCA-Based Database Mining Enables the Discovery of Bacterial Carbene Transferases for Stereodivergent Cyclopropanation.Angewandte Chemie (International ed. in English) · 2026Article
- Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.bioRxiv : the preprint server for biology · 2026Article
- Engineering a cytochrome P450 enzyme as a peroxygenase for selective hydroxylation of steroids.Nature communications · 2026Article
412 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.