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Mapping Dysfunctional Protein-Protein Interactions in Disease
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Published on: October 24, 2025

Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering

Jherome Brylle Woody Santos1, Jeremy M G Leung2, Lillian T Chong2

  • 1Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida, 32611, USA.

Biorxiv : the Preprint Server for Biology
|June 4, 2026
PubMed
Summary
This summary is machine-generated.

We developed Pathway Representation via Intrinsic Structural Medoids (PRISM) to cluster biomolecular transition pathways from simulations. PRISM effectively organizes complex conformational changes using representative structural states.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Molecular Dynamics Simulations

Background:

  • Analyzing complex biomolecular transitions requires robust methods to cluster simulation pathways.
  • Existing methods may struggle with sensitivity to outliers or computational scalability.

Purpose of the Study:

  • To introduce Pathway Representation via Intrinsic Structural Medoids (PRISM), a novel framework for clustering pathways from molecular dynamics simulations.
  • To provide a scalable and robust method for organizing and analyzing biomolecular transition pathways.

Main Methods:

  • PRISM maps pathways to structural medoids using k-means clustering.
  • It computes pathway dissimilarities using a weighted average Hausdorff distance between medoid sets.
  • Hierarchical agglomerative clustering is applied to group similar pathways into families.

Main Results:

  • PRISM demonstrated robust cluster assignments across three diverse biomolecular transitions.
  • The identified medoids accurately represent distinct conformational states within the pathways.
  • The framework effectively captures mean nearest-neighbor structural deviations while mitigating outlier sensitivity.

Conclusions:

  • PRISM offers a scalable framework for organizing complex transition pathways in biomolecular simulations.
  • The combination of state-based representation and geometric dissimilarities enhances pathway analysis.
  • PRISM facilitates a deeper understanding of conformational dynamics in biological systems.