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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Protein Networks02:26

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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PrePPI - Structure-based Prediction of Protein-protein Interactomes and Networks.

Caroline Velez1, Aniket Naravane1, Victor I Robila1

  • 1Department of Systems Biology, Columbia University Irving Medical Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA.

Journal of Molecular Biology
|March 1, 2026
PubMed
Summary
This summary is machine-generated.

PrePPI predicts protein-protein interactions (PPIs) using a structure-based pipeline. Newly clustered interactomes reveal functional subnetworks, offering new biological discovery pathways.

Keywords:
biological networksinteractome predictionprotein–protein interactionsshort linear motifs

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Area of Science:

  • Proteomics
  • Structural Biology
  • Bioinformatics

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Predicting PPIs aids in understanding biological pathways and disease mechanisms.
  • Structure-based approaches offer high accuracy in PPI prediction.

Purpose of the Study:

  • To present an expanded and redesigned PrePPI website for predicting protein-protein interactions.
  • To introduce novel clustering of interactomes based on structural likelihood.
  • To provide a proteome-wide view of functionally coherent PPI subnetworks.

Main Methods:

  • Utilizing a structure-based computational pipeline (PrePPI) for proteome-wide PPI prediction.
  • Integrating domain-domain and domain-short linear motif (SLiM) interactions.
  • Clustering predicted interactomes based on structure-based interaction likelihood.

Main Results:

  • The PrePPI resource now covers human, yeast, and E. coli proteomes.
  • 3D models for domain-level complexes and PDB templates for SLiM interactions are available.
  • Clustered interactomes demonstrate remarkable functional coherence, revealing biological subnetworks.

Conclusions:

  • The enhanced PrePPI website provides a powerful tool for biological discovery.
  • Structure-based PPI prediction and clustering offer unprecedented insights into cellular organization.
  • The resource facilitates exploration of protein interaction networks and their functional implications.