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...

Multi-Step Reactions

Multi-Step Reactions

Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...

Coupled Reactions

Coupled Reactions

Cellular processes such as building and breaking down complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Cells often couple the energy-releasing reaction with the energy-requiring one to carry out important cell functions.
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions....

Synthesis and Decomposition Reactions

Synthesis and Decomposition Reactions

Synthesis and decomposition are two types of redox reactions. Synthesis means to make something, whereas decomposition means to break something. The reactions are accompanied by chemical and energy changes.

Predicting Reaction Outcomes

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...

Chemical Equilibria: Systematic Approach to Equilibrium Calculations

Chemical Equilibria: Systematic Approach to Equilibrium Calculations

Equilibrium calculations for systems involving multiple equilibria are often complex. For example, to calculate the solubility of a sparingly soluble salt in an aqueous solution in the presence of a common ion, one must consider all the equilibria in this solution. Calculations for these systems can be complicated and tedious, so a systematic approach with a series of steps is often helpful. The process is detailed below.
The first step is to identify all the chemical reactions involved, The...

You might also read

Related Articles

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

Sort by

Same author

Outside the niche: Gut microbiota relay psychological stress to hematopoietic stem cell dysfunction.

Cell stem cell·2026

Same author

Elucidating the interaction between pyrazine flavor compounds and coffee proteins: Insights from multiscale structural and molecular dynamics simulations.

Current research in food science·2026

Same author

Angelica dahurica alleviates migraine via ameliorating neuroinflammation and oxidative stress.

Journal of ethnopharmacology·2026

Same author

Encapsulation of stimuli-responsive dyes into metal-organic frameworks for highly efficient dynamic multi-color emission.

Chemical communications (Cambridge, England)·2026

Same author

Pilot Study of Gallic Acid Cream as a Potential Treatment for Plaque Psoriasis.

Journal of medicinal food·2026

Same author

Triangulating evidence for cardiometabolic Index: ROC cutoff, spline nonlinearity, and explainable machine learning for CVD high risk.

Frontiers in cardiovascular medicine·2026

Search research articles

Related Experiment Video

Updated: Jun 15, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

From reactants to products: computational methods for biosynthetic pathway design.

Shaozhen Ding¹, Dongliang Liu¹, Yu Tian¹

¹Department of Chemical and Biomolecular Engineering, School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China.

Synthetic and Systems Biotechnology

|June 13, 2025

Summary

This summary is machine-generated.

Designing biosynthetic pathways for synthetic biology is complex. This review covers computational tools for pathway design, including biological data, retrosynthesis, and enzyme engineering, to improve efficiency and accuracy.

Keywords:

Biological big-data Enzyme engineering Methods of retrosynthetic analysis

More Related Videos

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products

A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products

Published on: October 4, 2019

Related Experiment Videos

Last Updated: Jun 15, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products

A Customizable Approach for the Enzymatic Production and Purification of Diterpenoid Natural Products

Published on: October 4, 2019

Area of Science:

Synthetic biology
Metabolic engineering
Biotechnology

Background:

Synthetic biology aims to produce valuable compounds using enzymatic pathways.
Manual design of biosynthetic pathways is challenging and time-consuming.
Computational approaches have advanced pathway design significantly.

Purpose of the Study:

To review key computational tools for biosynthetic pathway design.
To highlight the integration of biological data, retrosynthesis, and enzyme engineering.
To enhance the efficiency and accuracy of pathway design in synthetic biology.

Main Methods:

Review of biological big data resources (compounds, reactions, enzymes).
Analysis of retrosynthesis methods for pathway prediction.
Discussion of enzyme engineering techniques using data mining.

Main Results:

Identification of key computational tools for pathway design.
Demonstration of how multi-dimensional data aids pathway prediction.
Highlighting the role of data mining in enzyme discovery and design.

Conclusions:

Integrating biological big data, retrosynthesis, and enzyme engineering improves pathway design.
Computational tools are essential for efficient and accurate biosynthetic pathway construction.
Advances in these areas accelerate the production of value-added compounds in synthetic biology.