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Updated: Jul 15, 2025
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
Published on: March 3, 2015
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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
Summary
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.
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.
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