Related Experiment Video
Updated: Oct 19, 2025
10:41
Capturing the Interaction Kinetics of an Ion Channel Protein with Small Molecules by the Bio-layer Interferometry Assay
Published on: March 7, 2018
8.4K
iCDI-W2vCom: Identifying the Ion Channel-Drug Interaction in Cellular Networking Based on word2vec and node2vec
Jie Zheng1, Xuan Xiao1, Wang-Ren Qiu1
1Department of Computer Engineering, Jingdezhen Ceramic Institute, Jingdezhen, China.
Frontiers in Genetics
|September 27, 2021
Summary
A new computational method, iCDI-W2vCom, accurately predicts ion channel-drug interactions using sequence-based data. This approach overcomes limitations of structure-based methods and offers improved performance for drug discovery.
Area of Science:
- Computational biology
- Drug discovery
- Bioinformatics
Background:
- Ion channels represent a major drug target family, crucial for treating diseases like Alzheimer's and diabetes.
- Existing computational methods for predicting ion channel-drug interactions often require known 3D structures, which are frequently unavailable.
- Sequence-based prediction methods are needed but often require improvement or lack accessible web servers.
Purpose of the Study:
- To develop an effective and efficient sequence-based computational method for predicting ion channel-drug interactions.
- To address the challenge of predicting interactions when 3D structures of ion channels are unknown.
- To provide an improved predictor that outperforms existing methods.
Main Methods:
- Developed a sequence-based classifier named iCDI-W2vCom.
- Formulated drug compounds using SMILES-word2vec, FP2-word2vec, SMILES-node2vec, and Extended Connectivity Fingerprints (ECFPs) into a 1184D vector.
- Represented ion channels using word2vec into a 64D vector.
- Employed the LightGBM classifier for the prediction engine.
Main Results:
- Achieved high accuracy of 91.95% and an Area Under the Curve (AUC) of 0.9703 via fivefold cross-validation.
- Demonstrated superior performance compared to existing predictors in the field of ion channel-drug interaction prediction.
- Established a user-friendly web server for the iCDI-W2vCom predictor.
Conclusions:
- iCDI-W2vCom is a highly accurate sequence-based method for predicting ion channel-drug interactions.
- The developed predictor offers a valuable tool for drug discovery, especially when 3D structural information is limited.
- The methodology shows potential for broader applications in predicting target-drug interactions.
More Related Videos
Related Concept Videos
02:26Protein Networks
4.2K
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,...
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,...
4.2K
01:19The Role of Ion Channels in Neuronal Computation
3.3K
A postsynaptic neuron usually receives numerous impulses from several other presynaptic neurons. The axon hillock of the postsynaptic neuron integrates all these signals and determines the likelihood of firing an action potential.
Sometimes a single EPSP is strong enough to induce an action potential in the postsynaptic neuron. However, multiple presynaptic inputs must often create EPSPs around the same time for the postsynaptic neuron to be sufficiently depolarized to fire an action potential....
Sometimes a single EPSP is strong enough to induce an action potential in the postsynaptic neuron. However, multiple presynaptic inputs must often create EPSPs around the same time for the postsynaptic neuron to be sufficiently depolarized to fire an action potential....
3.3K
01:17Pore Transport and Ion-Pair Transport
765
Pore transport and ion-pair formation are critical mechanisms for the absorption and distribution of drugs in the body.
Pore transport, also known as convective transport, is a process where small molecules like urea, water, and sugars rapidly cross cell membranes as though there were channels or pores in the membrane. Although direct microscopic evidence is limited but the concept of pores or channels is widely accepted based on physiological evidence. Despite the lack of direct...
Pore transport, also known as convective transport, is a process where small molecules like urea, water, and sugars rapidly cross cell membranes as though there were channels or pores in the membrane. Although direct microscopic evidence is limited but the concept of pores or channels is widely accepted based on physiological evidence. Despite the lack of direct...
765
01:19Facilitated Transport
15.3K
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...
15.3K
01:24Non-gated Ion Channels
7.5K
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....
Compared to the gated ion channels, the non-gated channels, also known as leakage or passive channels, have no gating mechanism....
7.5K
01:30Ligand-Gated Ion Channel Receptor: Gating Mechanism
3.0K
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...
3.0K