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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

4.9K
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...
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Ligand Binding Sites02:40

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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...
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Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

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Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Tissue-Drug Binding: Localization of Drugs and its Significance01:24

Tissue-Drug Binding: Localization of Drugs and its Significance

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Body tissues, comprising approximately 40% of the body weight, are crucial in drug distribution and localization. These tissues can serve as drug storage sites, competing with plasma binding sites for drug molecules.
Drugs can bind to different tissue components, enhancing their distribution and localization. The factors influencing drug localization in tissues include the drug's lipophilicity, structural characteristics, tissue perfusion rate, and pH differences. These factors determine...
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Related Experiment Video

Updated: Dec 3, 2025

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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Spatiotemporal identification of druggable binding sites using deep learning.

Igor Kozlovskii1, Petr Popov2

  • 1iMolecule, Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia.

Communications Biology
|October 28, 2020
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Summary

This study introduces BiteNet, a computational tool for identifying protein binding sites by treating protein structures as 3D images. BiteNet accurately and rapidly detects challenging allosteric binding sites, advancing drug discovery.

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Area of Science:

  • Computational biology
  • Structural biology
  • Drug discovery

Background:

  • Protein binding site identification is crucial for drug discovery.
  • Protein conformation influences binding site presence, posing a challenge for detection.
  • Existing methods may struggle with dynamic or allosteric sites.

Purpose of the Study:

  • To develop a novel computational approach for large-scale protein binding site detection.
  • To leverage computer vision principles for analyzing protein conformations.
  • To enable the identification of difficult-to-spot allosteric and conformation-specific binding sites.

Main Methods:

  • A computational method treating protein conformations as 3D images and binding sites as detectable objects.
  • Analysis of conformational ensembles as 3D videos.
  • Application of the BiteNet model for spatiotemporal binding site detection.

Main Results:

  • BiteNet successfully identified conformation-specific binding sites in epidermal growth factor receptor.
  • The method detected oligomer-specific binding sites in ion channels.
  • It also found binding sites in G protein-coupled receptors.
  • BiteNet demonstrated superior accuracy and speed compared to state-of-the-art methods, analyzing 1000 conformations in ~1.5 minutes.

Conclusions:

  • BiteNet offers an effective computational strategy for identifying diverse protein binding sites.
  • The approach expands the druggable genome by revealing novel binding opportunities.
  • BiteNet enhances drug discovery pipelines through accurate and rapid binding site detection.