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Background <p>The domain-linker-domain (DLD) architecture is commonly found in proteins, where flexible linkers connect consecutive domains and regulate their relative spatial positioning. Often, these linkers present partially structured elements that modulate inter-domain dynamics, directly influencing their function. From a protein design perspective, tuning the relative position and orientation of domains via the linker offers opportunities to modulate biological activity. Despite their relevance, analyzing conformational ensembles of DLD proteins remains a challenge, thereby limiting the structural insights that can be extracted.</p> Results <p>We present DL3D, a robotics-inspired visualization tool that enables intuitive analysis of the conformational space sampled by DLD proteins. DL3D discretizes the relative positions of the two domains at the linker ends and projects each conformation onto a 3D voxel map, where density is represented in grayscale to highlight the most probable configurations. In addition, quaternion-based operations allow the analysis of relative domain orientations.</p> Conclusion <p>DL3D facilitates the structural investigation of highly flexible proteins composed of well-folded domains connected by flexible linkers. Beyond visualization, the tool supports downstream analyses such as low-dimensional conformational clustering. DL3D is implemented as a Python package and is available at: <a href="https://gitlab.laas.fr/moma/methods/analysis/dl3d/">https://gitlab.laas.fr/moma/methods/analysis/dl3d/</a>. A Jupyter notebook with usage examples is also provided.</p>

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DL3D: visual representation of conformational ensembles of domain-linker-domain proteins

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月29日

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  • Laure Carrière,
  • Simon Bartels,
  • Christophe Zanon,
  • Pau Bernadó,
  • Juan Cortés

摘要

Background

The domain-linker-domain (DLD) architecture is commonly found in proteins, where flexible linkers connect consecutive domains and regulate their relative spatial positioning. Often, these linkers present partially structured elements that modulate inter-domain dynamics, directly influencing their function. From a protein design perspective, tuning the relative position and orientation of domains via the linker offers opportunities to modulate biological activity. Despite their relevance, analyzing conformational ensembles of DLD proteins remains a challenge, thereby limiting the structural insights that can be extracted.

Results

We present DL3D, a robotics-inspired visualization tool that enables intuitive analysis of the conformational space sampled by DLD proteins. DL3D discretizes the relative positions of the two domains at the linker ends and projects each conformation onto a 3D voxel map, where density is represented in grayscale to highlight the most probable configurations. In addition, quaternion-based operations allow the analysis of relative domain orientations.

Conclusion

DL3D facilitates the structural investigation of highly flexible proteins composed of well-folded domains connected by flexible linkers. Beyond visualization, the tool supports downstream analyses such as low-dimensional conformational clustering. DL3D is implemented as a Python package and is available at: https://gitlab.laas.fr/moma/methods/analysis/dl3d/. A Jupyter notebook with usage examples is also provided.