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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Predicting Reaction Outcomes02:24

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,...
Coupled Reactions01:17

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. 
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Multi-Step Reactions02:31

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...
Drug Metabolism: Phase I Reactions01:17

Drug Metabolism: Phase I Reactions

A phase I reaction is a biochemical process that introduces a functionally reactive polar group to a substance. This transformation predominantly occurs in the liver, facilitated by the cytochrome P450 system of hemoproteins situated in the lipophilic endoplasmic reticulum of cells. The metabolite generated through this process can have varying polarities. If it is sufficiently polar, it can be easily excreted in the urine due to its water compatibility. However, if the metabolite is nonpolar,...

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Related Experiment Video

Updated: May 8, 2026

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

Extracting reaction networks from databases-opening Pandora's box.

Liam G Fearnley, Melissa J Davis, Mark A Ragan

    Briefings in Bioinformatics
    |August 16, 2013
    PubMed
    Summary

    Pathway knowledge representation significantly impacts biological reaction network extraction. Different database formats dramatically affect signal transduction network analysis, crosstalk, and cell interaction modeling.

    Keywords:
    databasesmodellingreaction networkssignal transduction

    Related Experiment Videos

    Last Updated: May 8, 2026

    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

    Area of Science:

    • Bioinformatics
    • Systems Biology
    • Computational Biology

    Background:

    • Public databases store extensive biological pathway information.
    • Biologists use pathway databases for experimental interpretation and hypothesis generation.
    • Computational methods require standardized pathway descriptions for reaction network extraction.

    Purpose of the Study:

    • To systematically evaluate how common knowledge representations affect biological reaction network extraction.
    • To assess the impact of pathway representations on signal transduction network analysis.

    Main Methods:

    • Systematic evaluation of knowledge representations in pathway databases.
    • Analysis of reaction network extraction from signal transduction pathways.
    • Assessment of impacts on network connectivity, pathway crosstalk, and cell-cell interaction modeling.

    Main Results:

    • Extracting reaction networks from pathway databases is complex.
    • Pathway representations have significant consequences for network extraction and analysis.
    • The choice of representation impacts connectivity, crosstalk capture, and interaction modeling.

    Conclusions:

    • Researchers must consider knowledge representation issues for accurate computational modeling.
    • Standardized pathway descriptions are crucial for maximizing the value of pathway knowledge.
    • Understanding representation effects is key to reliable automated reaction network extraction.