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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,...
Ion Channels01:19

Ion Channels

The movement of ions like sodium, potassium, and calcium into and out of the cell is essential to maintain the electrochemical gradient in living cells. The ion channels—a class of membrane transport proteins—help maintain this ionic gradient for the smooth functioning of physiological activities such as maintaining cell size and volume, conducting nerve impulses, and gas and nutrient exchange.
Ion channels are specialized integral membrane proteins on the plasma membrane that allow specific...
Non-gated Ion Channels01:24

Non-gated Ion Channels

Ion channels are specialized proteins on the plasma membrane that allow charged ions to pass down their electrochemical gradient. Their main function is to maintain the membrane potential which is critical for cell viability. These channels are either gated or non-gated and can transport more than a thousand ions within milliseconds for the cellular event to occur.
Compared to the gated ion channels, the non-gated channels, also known as leakage or passive channels, have no gating mechanism.
Non-gated Ion Channels01:24

Non-gated Ion Channels

Ion channels are specialized proteins on the plasma membrane that allow charged ions to pass down their electrochemical gradient. Their main function is to maintain the membrane potential which is critical for cell viability. These channels are either gated or non-gated and can transport more than a thousand ions within milliseconds for the cellular event to occur.
Compared to the gated ion channels, the non-gated channels, also known as leakage or passive channels, have no gating mechanism.
Ligand-Gated Ion Channel Receptor: Gating Mechanism01:30

Ligand-Gated Ion Channel Receptor: Gating Mechanism

Ligand-gated ion channels are transmembrane proteins that play a vital role in intercellular communication and functions of the nervous system. They allow the influx of ions across the membrane once the neurotransmitter binds, allowing the subsequent transmission of electrical excitation across the neurons. Other ligand-gated ion channels, like the γ-aminobutyric acid (GABA) receptor, permit anions like chloride into the cells on the binding of the GABA molecule. Their entry into the cell...
Facilitated Transport01:19

Facilitated Transport

The chemical and physical properties of plasma membranes cause them to be selectively permeable. Since plasma membranes have both hydrophobic and hydrophilic regions, substances need to be able to transverse both regions. The hydrophobic area of membranes repels substances such as charged ions. Therefore, such substances need special membrane proteins to cross a membrane successfully. In  facilitated transport, also known as facilitated diffusion, molecules and ions travel across a membrane via...

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A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions
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ATDB 2.0: A database integrated toxin-ion channel interaction data.

Quanze He1, Wenjun Han, Quanyuan He

  • 1The Key Laboratory of Protein Chemistry and Developmental Biology of Ministry of Education, College of Life Sciences, Hunan Normal University, Changsha 410081, PR China.

Toxicon : Official Journal of the International Society on Toxinology
|August 3, 2010
PubMed
Summary
This summary is machine-generated.

The Animal Toxin Database (ATDB 2.0) is a new bioinformatics resource for studying toxin-channel interactions. It offers extensive data and a network browser to aid in predicting toxin functions.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Pharmacology

Background:

  • Animal toxins are crucial for understanding biological processes and developing therapeutics.
  • Analyzing toxin-channel interactions is complex due to data heterogeneity and scale.
  • Existing resources lack comprehensive, integrated data on these interactions.

Purpose of the Study:

  • To develop an updated and enhanced bioinformatics resource for toxin-channel interactions.
  • To provide a user-friendly platform for accessing and analyzing extensive T-C interaction data.
  • To facilitate sequence pattern recognition and functional prediction of novel toxins.

Main Methods:

  • Extraction, formatting, and mapping of over 54,000 toxin-channel interactions.
  • Integration of data into toxin and ion channel databases.
  • Development of a network browser for intuitive data exploration on the ATDB 2.0 website.

Main Results:

  • ATDB 2.0 now contains over 54,000 T-C interactions, with 9193 high-confidence entries.
  • A new network browser enables easy access and visualization of interaction data.
  • The database is mapped to established toxin and ion channel resources for enhanced utility.

Conclusions:

  • ATDB 2.0 serves as a valuable bioinformatics resource for T-C interaction analysis.
  • The resource facilitates research in sequence pattern recognition and functional prediction of toxins.
  • This updated database supports advancements in toxicology and drug discovery.