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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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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.
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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.
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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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The Equilibrium Binding Constant and Binding Strength02:18

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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:
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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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Related Experiment Video

Updated: May 27, 2025

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
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RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking.

Yaroslav Balytskyi, Inna Hubenko, Alina Balytska

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    |February 20, 2025
    PubMed
    Summary
    This summary is machine-generated.

    We developed RAPID-Net, a novel pocket-finding algorithm that improves drug docking accuracy. It outperforms existing methods and enables docking on large proteins, offering a competitive alternative for drug discovery.

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    Area of Science:

    • Computational chemistry
    • Structural biology
    • Drug discovery

    Background:

    • Accurate identification of druggable pockets is crucial for structure-based drug design.
    • Current algorithms often prioritize geometry over docking performance, limiting their utility.

    Purpose of the Study:

    • To develop RAPID-Net, a pocket-finding algorithm designed for seamless integration with docking workflows.
    • To enhance the accuracy and efficiency of structure-based drug design.

    Main Methods:

    • Developed RAPID-Net, a novel pocket-finding algorithm.
    • Evaluated RAPID-Net's performance against DiffBindFR, PUResNet, and Kalasanty on diverse datasets (PoseBusters, Astex Diverse Set, BU48, Coach420).
    • Assessed docking accuracy and pocket-ligand intersection rates, including comparisons with AlphaFold 3.

    Main Results:

    • RAPID-Net outperforms DiffBindFR on the PoseBusters benchmark when guiding AutoDock Vina.
    • RAPID-Net enables blind docking on large proteins unsuitable for AlphaFold 3.
    • RAPID-Net surpasses PUResNet and Kalasanty in docking accuracy and pocket-ligand intersection rates.
    • RAPID-Net shows competitive performance against AlphaFold 3 on the PoseBusters benchmark for pose identification.

    Conclusions:

    • RAPID-Net offers a cost-effective and competitive alternative to existing methods for structure-based drug design.
    • The algorithm demonstrates potential for identifying remote functional sites, aiding in the development of novel therapeutics.
    • Further improvements are possible with advanced pose reweighting tools.