ArticleNature methods2023
EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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
10 citing papers in PubMed.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Mechanism-informed rules tunably balance novelty and feasibility of predicted enzymatic reactions.bioRxiv : the preprint server for biology · 2026Article
- MechFind: a computational framework for de novo prediction of enzyme mechanisms.Nature communications · 2026Article
- MechFind: A computational framework for de novo prediction of enzyme mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Measuring catalytic mechanism similarity - a new approach to study enzyme function and evolution.The FEBS journal · 2025Article
- Paradigms of convergent evolution in enzymes.The FEBS journal · 2025Article
- Seven critical challenges in synthetic one-carbon assimilation and their potential solutions.FEMS microbiology reviews · 2025Review
- Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites.Nature communications · 2024Article
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- Using mechanism similarity to understand enzyme evolution.Biophysical reviews · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as 'Easy' Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literature on both related and unrelated enzymes. We validated EzMechanism on a set of 62 enzymes and have identified paths for further improvement, including the need for additional and more generic catalytic rules.
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.