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Related Concept Videos

Protein-protein Interfaces02:04

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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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Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Updated: Jul 15, 2025

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
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ZEPPI: proteome-scale sequence-based evaluation of protein-protein interaction models.

Haiqing Zhao1, Diana Murray1, Donald Petrey1

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

Research Square
|October 4, 2023
PubMed
Summary
This summary is machine-generated.

We developed ZEPPI (Z-score Evaluation of Protein-Protein Interfaces), a new scoring framework for protein complex structural models. ZEPPI uses sequence co-evolution to assess protein-protein interfaces, improving model evaluation.

Keywords:
Protein-protein interactionscoevolutionprotein complex predictionprotein structure

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Evaluating the accuracy of protein complex structural models is crucial for understanding biological functions.
  • Existing methods may struggle with indirect interactions or require extensive sequence data.

Approach:

  • ZEPPI (Z-score Evaluation of Protein-Protein Interfaces) is a novel framework utilizing sequence co-evolution and conservation.
  • It specifically analyzes residues within protein-protein interfaces.
  • The ZEPPI score compares interface metrics to random residue sets, simplifying interaction analysis.

Key Points:

  • ZEPPI effectively evaluates protein-protein interfaces in structural models.
  • It leverages shallow sequence alignments by focusing on interfacial residues.
  • Performance is validated against known complexes and CASP-CAPRI decoys.

Conclusions:

  • ZEPPI offers a scalable solution, demonstrated by proteome-wide calculations on millions of models.
  • This framework can generate novel hypotheses regarding protein complex function.