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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

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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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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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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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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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Protein Networks02:26

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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.
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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis.

Lukáš Polák1, Petr Škoda1, Kamila Riedlová1

  • 1Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, 121 16, Czech Republic.

Nucleic Acids Research
|May 19, 2025
PubMed
Summary

PrankWeb's updated version enhances protein-ligand binding site (LBS) prediction by introducing modular postprocessing and visualization capabilities. This allows for molecule docking and interactive pose viewing, improving biological understanding and drug discovery.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Protein-ligand binding sites (LBSs) are critical for biological understanding and applications in medicine and biotechnology.
  • Accurate prediction of LBSs is essential for rational drug design and molecular modeling.
  • Existing tools require enhancement for advanced postprocessing and visualization of predicted binding sites.

Purpose of the Study:

  • To introduce a new, modular version of the PrankWeb server for enhanced protein-ligand binding site prediction.
  • To integrate client- and server-side modules for postprocessing predicted pockets and molecule docking.
  • To improve user interaction and visualization of prediction results, including molecular poses.

Main Methods:

  • Development of a modular architecture for PrankWeb, supporting client- and server-side postprocessing modules.
  • Integration of AutoDock Vina for server-side molecule docking into predicted pockets.
  • Implementation of visualization modules for interactive display of predicted poses and results.
  • Revamping the PrankWeb interface for better module support and user interaction between 1D and 3D viewers.
  • Introduction of a faster P2Rank backend and user-friendly exports like ChimeraX visualization.

Main Results:

  • The new PrankWeb version enables flexible postprocessing and visualization of predicted protein-ligand binding sites.
  • Users can now dock molecules into predicted pockets and interactively visualize the resulting poses.
  • Enhanced user interface improves interaction between 1D and 3D viewers for better data exploration.
  • Faster P2Rank backend and improved export options streamline the analysis workflow.

Conclusions:

  • The modular PrankWeb system offers a powerful and flexible platform for protein-ligand binding site prediction and analysis.
  • The integrated docking and visualization capabilities facilitate drug discovery and molecular modeling research.
  • The updated PrankWeb server enhances usability and efficiency for researchers in computational biology and related fields.