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DockIT: a tool for interactive molecular docking and molecular complex construction.

Georgios Iakovou1,2, Mousa Alhazzazi1, Steven Hayward1

  • 1School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK.

Bioinformatics (Oxford, England)
|December 28, 2020
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Summary
This summary is machine-generated.

DockIT is an interactive molecular docking tool enabling users to precisely position ligands and receptors using physical and graphical features. This facilitates the creation of accurate molecular models for simulations by ensuring physically feasible docking poses.

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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Molecular docking is crucial for understanding ligand-receptor interactions.
  • Accurate modeling of these interactions is essential for drug design and systems biology.
  • Existing tools may lack the necessary physical and interactive features for precise pose generation.

Purpose of the Study:

  • To introduce DockIT, a novel interactive molecular docking tool.
  • To enable users to achieve physically feasible docking poses with enhanced control.
  • To facilitate the construction of complex molecular systems for simulation.

Main Methods:

  • Interactive manipulation of ligand and receptor positioning and orientation via mouse/keyboard or haptic device.
  • Utilizing molecular dynamics-based force fields to model atomic interactions and forces.
  • Real-time calculation and visualization of intermolecular hydrogen bonds and collision detection.
  • Monitoring of intermolecular atomic distances for constraint satisfaction.

Main Results:

  • DockIT allows users to intuitively guide ligands into receptors, feeling forces via a haptic device.
  • The tool provides real-time feedback on atomic interactions, hydrogen bonds, and collisions.
  • Physically plausible docking poses can be generated and validated against experimental constraints.
  • The software supports the creation and saving of multi-component structures for further simulation.

Conclusions:

  • DockIT offers a unique combination of physical and graphical features for interactive molecular docking.
  • It empowers users to generate accurate and physically valid docking poses.
  • The tool streamlines the preparation of molecular systems for molecular dynamics simulations.