Related Experiment Video
Updated: Feb 8, 2026
11:39
Identification of Functional Protein Regions Through Chimeric Protein Construction
Published on: January 8, 2019
11.0K
Identification and visualization of protein binding regions with the ArDock server
Sébastien Reille1, Mélanie Garnier1, Xavier Robert1
1Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, 69367 Lyon Cedex 07, France.
Nucleic Acids Research
|June 16, 2018
Summary
ArDock predicts protein interaction sites by analyzing surface residue tendencies in docking experiments. This structural bioinformatics tool visualizes potential protein interfaces for further research.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein-protein interactions
Background:
- Protein surfaces contain regions prone to interaction.
- Predicting these interaction sites is crucial for understanding protein function.
- Existing methods may not fully capture the complexity of protein interfaces.
Purpose of the Study:
- To develop and present ArDock, a web server for predicting and visualizing protein interaction regions.
- To rank surface residues based on their likelihood of forming protein interfaces.
- To provide a tool for identifying potential interaction sites, including alternate interfaces.
Main Methods:
- Utilizing a methodology derived from large-scale cross-docking studies.
- Analyzing the tendency of proteins to dock in non-random ways at surfaces.
- Inputting protein structures to compute scores for each surface residue.
Main Results:
- ArDock successfully ranks surface residues by their interface-forming potential.
- The server identifies potential interaction sites on protein surfaces.
- It can predict alternate interfaces for proteins with multiple interaction modes.
Conclusions:
- ArDock offers a valuable tool for predicting and visualizing protein interaction sites.
- The server enhances understanding of protein-protein interactions through structural analysis.
- ArDock facilitates further research in structural bioinformatics and drug discovery.
More Related Videos
Related Concept Videos
01:49Conserved Binding Sites
5.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.2K
01:20Factors Affecting Protein-Drug Binding: Protein-Related Factors
575
Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
The physicochemical properties of a drug play a significant role in its ability to bind to proteins. Lipophilic drugs, which dissolve in fats, oils, and lipids, can be...
The physicochemical properties of a drug play a significant role in its ability to bind to proteins. Lipophilic drugs, which dissolve in fats, oils, and lipids, can be...
575
02:18The Equilibrium Binding Constant and Binding Strength
15.1K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
15.1K
02:40The Eukaryotic Promoter Region
18.9K
The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
18.9K
02:40Ligand Binding Sites
15.1K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
15.1K
01:29Drug Distribution: Plasma Protein Binding
9.0K
Drugs predominantly attach to plasma proteins, with only a small percentage remaining unbound. The unbound portion can be calculated as one minus the bound fraction. Acidic drugs form large, inactive complexes by reversibly binding to plasma albumin, which prevents them from diffusing across biological barriers. These drug-protein complexes act as reservoirs for the drugs. As the concentration of unbound drugs decreases, these complexes quickly dissociate to release the free drug, maintaining...
9.0K