Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

Biosynthesis in Bacteria

Biosynthesis in Bacteria

Biosynthesis in bacteria is a fundamental anabolic process that generates essential macromolecules, including proteins, nucleic acids, lipids, and polysaccharides. These macromolecules are critical for cellular growth, replication, and function. The process is tightly regulated and energetically linked to catabolic pathways to ensure optimal resource utilization.Biosynthetic pathways begin with precursor metabolites such as pyruvate, acetyl-CoA, and glucose-6-phosphate derived from glycolysis,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Off the beaten (catalytic) path: Charting the mechanistic space of enzyme reactions.

The Journal of chemical physics·2025

Same author

Measuring catalytic mechanism similarity - a new approach to study enzyme function and evolution.

The FEBS journal·2025

Same author

A structural perspective on enzymes and their catalytic mechanisms.

Current opinion in structural biology·2025

Same author

Paradigms of convergent evolution in enzymes.

The FEBS journal·2024

Same author

Enzyme function and evolution through the lens of bioinformatics.

The Biochemical journal·2023

Same author

EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions.

Nature methods·2023

Search research articles

Related Experiment Video

Updated: Jan 5, 2026

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

Exploring Chemical Biosynthetic Design Space with Transform-MinER.

Jonathan D Tyzack¹, Antonio J M Ribeiro¹, Neera Borkakoti¹

¹European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton CB10 1SD , United Kingdom.

ACS Synthetic Biology

|October 25, 2019

Summary

Transform-MinER is a web tool for exploring enzyme reactions and chemical space. It aids enzyme design and directed evolution by identifying promising molecular starting points with 90% success.

Keywords:

chemoinformatics data-mining enzyme design molecular fingerprints promiscuity synthetic biology

More Related Videos

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

A High-Yield Streptomyces Transcription-Translation Toolkit for Synthetic Biology and Natural Product Applications

A High-Yield Streptomyces Transcription-Translation Toolkit for Synthetic Biology and Natural Product Applications

Published on: September 10, 2021

Related Experiment Videos

Last Updated: Jan 5, 2026

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Mass Spectrometry-Guided Genome Mining as a Tool to Uncover Novel Natural Products

Published on: March 12, 2020

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Efficient Sampling of Genetically Encoded Biosensor Design Space Enabled with a Design of Experiments and Automation Workflow

Published on: October 17, 2025

A High-Yield Streptomyces Transcription-Translation Toolkit for Synthetic Biology and Natural Product Applications

A High-Yield Streptomyces Transcription-Translation Toolkit for Synthetic Biology and Natural Product Applications

Published on: September 10, 2021

Area of Science:

Biochemistry
Computational Chemistry
Synthetic Biology

Background:

Exploring chemical biosynthetic space is crucial for enzyme design.
Directed evolution experiments require efficient methods to identify novel enzymatic pathways.
Current tools may lack comprehensive approaches for navigating complex molecular transformations.

Purpose of the Study:

To introduce Transform-MinER, a web application for exploring chemical biosynthetic space.
To guide users toward optimal starting points for enzyme design and directed evolution.
To present a novel ligand-based methodology for enzyme reaction prediction.

Main Methods:

Transform-MinER employs two search functionalities: Molecule Search and Path Search.
Chemoinformatic fingerprints are utilized to identify reaction centers in substrates.
The methodology prioritizes reactions that move closer to a target molecule using native-like transformations.

Main Results:

Transform-MinER achieved a 90% success rate in identifying valid enzyme reactions.
Performance was validated using native pathways from the KEGG database.
The tool demonstrated effectiveness on a dataset of *de novo* enzyme reactions.

Conclusions:

Transform-MinER provides a powerful platform for exploring enzymatic transformations.
The application effectively aids in enzyme design and directed evolution strategies.
The validated 90% success rate highlights the robustness of the underlying methodology.