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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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DDtrek: A PyMOL-Based Management System for 3D Structural Data Series.

Evgenii M Osipov1, Sergei V Strelkov1

  • 1Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49, Box 822, 3000 Leuven, Belgium.

ACS Omega
|June 9, 2025
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Summary
This summary is machine-generated.

DDtrek is a new PyMOL plugin for aligning and evaluating biomacromolecular structures. It aids structure-based drug design by visualizing ligands and experimental density maps for model reliability assessment.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Drug Design

Background:

  • Researchers often generate series of related biomacromolecular structures.
  • Structure-based drug design requires analyzing protein-ligand complexes.

Purpose of the Study:

  • Introduce DDtrek, a system for alignment, evaluation, and presentation of structural data.
  • Facilitate the assessment of atomic model reliability and partial disorder.

Main Methods:

  • DDtrek is implemented as a plugin for PyMOL.
  • Visualizes aligned ligand structures with experimental density maps (X-ray crystallography, cryo-electron microscopy).

Main Results:

  • DDtrek provides a system for alignment, evaluation, and presentation of structural data.
  • Enables visualization of ligands alongside experimental density maps.
  • Offers assessment of atomic model reliability and partial disorder.

Conclusions:

  • DDtrek is a lightweight, user-friendly system for research teams.
  • Facilitates structure-based drug design and structural data analysis.
  • Freely available for Windows, MacOS, and Linux.