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Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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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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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Flexible Protein-Protein Docking with SwarmDock.

Iain H Moal1, Raphael A G Chaleil2, Paul A Bates2

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. moal@ebi.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|April 2, 2018
PubMed
Summary

Computational protein docking models complex structures when experimental data is limited. This guide details using SwarmDock for protein-protein docking, covering pose generation, analysis, and validation for applications in drug design and systems biology.

Keywords:
Computational chemistryDockingMolecular modellingProtein-protein interaction

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Area of Science:

  • Structural biology
  • Computational chemistry
  • Bioinformatics

Background:

  • Experimental determination of protein complex atomic structures is challenging but crucial for drug design, protein engineering, systems biology, and understanding disease.
  • Computational modeling offers a viable alternative when experimental structures are unavailable, provided subunit structures are known.

Purpose of the Study:

  • To provide practical guidelines for protein-protein docking using the SwarmDock flexible docking method.
  • To outline key considerations for successful docking, including input preparation, pose generation, and model validation.

Main Methods:

  • Utilizes the SwarmDock algorithm for flexible protein-protein docking.
  • Covers essential steps: preparing structural input, generating docked poses, and analyzing/ranking these poses.
  • Emphasizes model validation using external data.

Main Results:

  • Presents a comprehensive workflow for computational protein docking.
  • Offers insights into factors influencing docking success.
  • Demonstrates the application of SwarmDock for modeling protein complexes.

Conclusions:

  • SwarmDock provides a practical approach to modeling protein complex structures computationally.
  • Effective docking requires careful consideration of input preparation, pose generation, and rigorous validation.
  • Computational docking is a valuable tool complementing experimental methods in structural biology and drug discovery.