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Updated: Jan 10, 2026

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Dockground: Expanding the Resource to Protein-DNA Complexes.

Keeley W Collins1, Matthew M Copeland1, Petras J Kundrotas1

  • 1Computational Biology Program, The University of Kansas, Lawrence, KS 66045, United States.

Journal of Molecular Biology
|November 22, 2025
PubMed
Summary
This summary is machine-generated.

The Dockground project now includes protein-DNA interactions, offering crucial data for computational modeling of molecular mechanisms. This resource aids in understanding cellular processes and developing new structure-based modeling techniques.

Keywords:
molecular databasesmolecular recognitionprotein dockingprotein-DNA complexesstructural modeling

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Molecular Biology

Background:

  • Protein-DNA interactions are fundamental to essential cellular processes like replication, transcription, and DNA repair.
  • Experimentally determining the structures of protein-nucleic acid complexes is challenging due to their instability, resulting in limited available data.
  • Computational modeling is vital for understanding biomolecular mechanisms and predicting molecular interactions.

Purpose of the Study:

  • To expand the Dockground resource to include protein-DNA complexes, enhancing knowledge of macromolecular interfaces.
  • To provide a data resource for developing and improving structure-based modeling techniques for macromolecular interactions.
  • To offer new features including automatic weekly updates and a user-friendly web interface for protein-DNA complex data.

Main Methods:

  • Expansion of the Dockground database to incorporate protein-DNA complexes.
  • Implementation of automatic weekly update procedures for the resource.
  • Development of a user-friendly web interface for searching, analyzing, and downloading complex data.

Main Results:

  • The Dockground resource now comprehensively covers protein-protein, protein-RNA, and protein-DNA interactions.
  • New automated updates and an enhanced web interface improve accessibility and utility for researchers.
  • The resource's utility was demonstrated by benchmarking AlphaFold3 predictions against the protein-DNA complex data.

Conclusions:

  • The expanded Dockground resource significantly advances the study of macromolecular interactions, particularly protein-DNA complexes.
  • This resource is essential for computational modeling, aiding in the understanding and potential modulation of key cellular processes.
  • Dockground serves as a valuable, publicly accessible data repository for the structural biology and computational modeling communities.