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Related Experiment Video

Updated: Sep 11, 2025

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P4ward: An Automated Modeling Platform for Protac Ternary Complexes.

Paula Jofily1, Subha Kalyaanamoorthy1,2,3

  • 1Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

Journal of Chemical Information and Modeling
|August 13, 2025
PubMed
Summary
This summary is machine-generated.

P4ward is a new automated tool for modeling Proteolysis Targeting Chimeras (Protacs) ternary complexes. This free pipeline significantly improves modeling accuracy, aiding in the rational design and discovery of novel Protac therapeutics.

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Drug Discovery

Background:

  • Proteolysis Targeting Chimeras (Protacs) leverage the ubiquitin-proteasome system for targeted protein degradation.
  • Rational design of Protacs necessitates accurate structural models of E3 ligase:Protac:protein of interest ternary complexes.
  • Computational modeling of these heteromeric complexes presents significant challenges, with a need for improved accuracy and speed.

Purpose of the Study:

  • To develop a free, automated computational pipeline for modeling Protac ternary complexes.
  • To enhance the accuracy and efficiency of Protac ternary complex structure prediction.
  • To support the screening phase of Protac discovery and accelerate therapeutic development.

Main Methods:

  • Development of P4ward, a fully automated Protac ternary complex modeling pipeline.
  • Utilized computational approaches to predict heteromeric complex structures.
  • Evaluated pipeline performance against existing methods for accuracy and speed.

Main Results:

  • P4ward achieved a 76.5% hit rate with an average rank of 7.26.
  • Demonstrated substantial improvement in ranking near-native poses by 73-98% compared to previous programs.
  • The pipeline offers a user-friendly, fast, and effective solution for Protac modeling.

Conclusions:

  • P4ward provides a significant advancement in computational modeling for Protac rational design.
  • The tool offers atomistic insights crucial for optimizing Protac therapeutics.
  • P4ward is poised to accelerate the discovery and development of novel Protac-based drugs.