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Related Experiment Video

Updated: Jan 20, 2026

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Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking.

Kathryn A Porter1, Dzmitry Padhorny2,3, Israel Desta1

  • 1Department of Biomedical Engineering, Boston University, Boston, Massachusetts.

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|August 25, 2019
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Summary

The ClusPro server now includes template-based modeling (TBM) for improved protein complex prediction accuracy. This new feature enhances model quality, especially when suitable templates are available, building on previous successes.

Keywords:
homology modelingmethod developmentmodeling of protein complexesprotein-protein interactiontemplate-based

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • The ClusPro server has historically used free docking of homology models for protein complex prediction.
  • Previous CASP-CAPRI assessments highlighted the potential of template-based methods for higher-quality models when templates exist.

Purpose of the Study:

  • To introduce and review the new template-based modeling (TBM) functionality in the ClusPro server.
  • To enhance the accuracy and quality of protein complex predictions, particularly for targets with available templates.

Main Methods:

  • Integration of a new template-based modeling (TBM) module into the ClusPro web server.
  • Utilizing existing template information to guide protein-protein docking and model generation.

Main Results:

  • The ClusPro TBM functionality has expanded the server's capability to generate higher-accuracy predictions.
  • Template-based methods demonstrated a higher yield of medium-quality models for targets with good templates compared to previous free docking approaches.
  • Improvements were observed for both homomeric and some heteromeric protein targets.

Conclusions:

  • The addition of ClusPro TBM significantly improves protein complex prediction accuracy, especially when templates are available.
  • Ongoing development focuses on refining TBM and incorporating co-evolutionary data for enhanced free docking.
  • The ClusPro server continues to evolve based on performance in assessments like CASP-CAPRI.