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Related Concept Videos

The Equilibrium Binding Constant and Binding Strength02:18

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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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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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PoseFilter: a PyMOL plugin for filtering and analyzing small molecule docking in symmetric binding sites.

Justine C Williams1, Subha Kalyaanamoorthy1

  • 1Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada.

Bioinformatics (Oxford, England)
|March 20, 2021
PubMed
Summary
This summary is machine-generated.

PoseFilter, a new PyMOL plugin, aids in analyzing and filtering protein-ligand docking poses. It automates symmetric pose detection and offers root mean square deviation and interaction fingerprint analyses.

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Drug Discovery

Background:

  • Protein-ligand docking is crucial for drug discovery.
  • Analyzing large numbers of docked poses can be challenging.
  • Identifying symmetric poses is important for oligomeric complexes.

Purpose of the Study:

  • To introduce PoseFilter, a novel PyMOL plugin.
  • To facilitate the analysis and filtering of docked poses.
  • To enable automatic detection of symmetric poses.

Main Methods:

  • PoseFilter is a PyMOL plugin with a graphical user interface and command-line options.
  • It implements methods for root mean square deviation (RMSD) analysis.
  • It incorporates interaction fingerprint analysis for pose comparison.

Main Results:

  • PoseFilter successfully automates the detection of symmetric poses.
  • The plugin provides robust tools for analyzing docking outputs.
  • Its capabilities are demonstrated on various oligomeric protein-ligand complexes.

Conclusions:

  • PoseFilter streamlines the analysis of protein-ligand docking poses.
  • The plugin enhances the efficiency of virtual screening workflows.
  • It is a valuable tool for researchers in computational chemistry and drug design.