Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

11.4K
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,...
11.4K
Chemical Reactions01:19

Chemical Reactions

97.6K
A chemical reaction is a process by which the bonds in the atoms of substances are rearranged to generate new substances. Matter cannot be created or destroyed in a chemical reaction—the same type and number of atoms that make up the reactants are still present in the products. Merely, the rearrangement of chemical bonds produces new compounds.
Chemical Reactions Rearrange Atoms into New Substances
A chemical reaction takes starting materials—the reactants—and changes them...
97.6K
Chemical Reactions02:26

Chemical Reactions

13.9K
A balanced chemical equation provides the information of chemical formulas of the reactants and products involved in the chemical change. A reaction’s stoichiometry helps predict how much of the reactant is needed to produce the desired amount of product, or in some cases, how much product will be formed from a specific amount of the reactant.
The relative amounts of reactants and products represented in a balanced chemical equation are often referred to as stoichiometric amounts. However, in...
13.9K
Synthesis and Decomposition Reactions02:17

Synthesis and Decomposition Reactions

39.1K
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. 
39.1K
Classification of Titrimetric Analysis Based on Reaction Types01:01

Classification of Titrimetric Analysis Based on Reaction Types

2.0K
Titrimetric analysis in solution chemistry involves measuring the volume of solutions and is often called volumetric analysis. The standard solution of known concentration in the burette is called the titrant, whereas the solution of unknown concentration in the flask is called the analyte, or titrand. Titrimetric analyses can be classified into four types based on the reactions between the titrant and analyte.
Titrations between an acid and a base lead to neutralization reactions that form...
2.0K
Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

22.0K
Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
22.0K

You might also read

Related Articles

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

Sort by
Same author

RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.

NAR genomics and bioinformatics·2026
Same author

Bioinformatics strategies and biomarker refinement using high-throughput transcriptome data in transplantation.

Frontiers in bioinformatics·2026
Same author

Biophysical Modeling Elucidates Mechanistic Principles for Rational Molecular Glue Design.

Journal of chemical information and modeling·2026
Same author

Locus-specific proteomics identifies novel regulators of Epstein-Barr virus lytic reactivation.

Journal of virology·2026
Same author

Chronic graft-versus-host disease suppressing CD56<sup>bright</sup>Perforin<sup>neg</sup> regulatory-like NK cells inhibit CD4<sup>+</sup> T cells via PD-1, LAG-3, and TRAIL.

Cytotherapy·2026
Same author

RP3Net: a deep learning model for predicting recombinant protein production in Escherichia coli.

Bioinformatics (Oxford, England)·2026

Related Experiment Video

Updated: Mar 21, 2026

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers
08:51

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers

Published on: August 18, 2017

11.0K

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Syed Asad Rahman1, Gilliean Torrance2, Lorenzo Baldacci3

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Congenica Ltd, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

Bioinformatics (Oxford, England)
|May 7, 2016
PubMed
Summary

Reaction Decoder is a command-line tool that accurately extracts chemical features like Atom-Atom Mapping (AAM) and Bond Changes (BCs) from biochemical reactions. This software aids in analyzing metabolic pathways and comparing chemical reactions.

More Related Videos

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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

Published on: February 8, 2017

18.7K
High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

4.4K

Related Experiment Videos

Last Updated: Mar 21, 2026

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers
08:51

Coulomb Explosion Imaging as a Tool to Distinguish Between Stereoisomers

Published on: August 18, 2017

11.0K
A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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

Published on: February 8, 2017

18.7K
High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

4.4K

Area of Science:

  • Biochemistry
  • Computational Chemistry

Background:

  • Understanding enzymatic reactions requires detailed chemical feature extraction.
  • Key features include Atom-Atom Mapping (AAM), Bond Changes (BCs), and Reaction Centres.

Purpose of the Study:

  • To introduce Reaction Decoder, a robust command-line tool for accurate chemical feature extraction from biochemical reactions.
  • To facilitate the analysis of metabolic pathways and comparative studies of chemical reactions.

Main Methods:

  • The Reaction Decoder tool computes AAM and highlights BCs.
  • It supports standard chemical input/output formats like RXN/SMILES.
  • The software generates images of mapped reactions for visual analysis.

Main Results:

  • High accuracy in computing AAM and identifying BCs.
  • Successful generation of reaction images for enhanced visualization.
  • Support for multiple chemical file formats.

Conclusions:

  • Reaction Decoder provides a powerful and accurate method for extracting critical chemical information from biochemical reactions.
  • The tool aids researchers in metabolic pathway analysis and comparative reaction studies.