Related Experiment Video

Updated: May 14, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

PPIFold: a tool for analysis of protein-protein interaction from AlphaPullDown

Quentin Rouger¹, Emmanuel Giudice¹, Damien F Meyer^2,3

¹Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR)-UMR6290, Rennes 35000, France.

Bioinformatics Advances

|May 12, 2025

Abstract

Motivation:

Protein structure and protein-protein interaction (PPI) predictions based on coevolution have transformed structural biology, but managing pre-processing and post-processing can be complex and time-consuming, making these tools less accessible.

Results:

Here, we introduce PPIFold, a pipeline built on the AlphaPulldown Python package, designed to automate file handling and streamline the generation of outputs, facilitating the interpretation of PPI prediction results. The pipeline was validated on the bacterial Type 4 Secretion System nanomachine, demonstrating its effectiveness in simplifying PPI analysis and enhancing accessibility for researchers.

Availability And Implementation:

PPIFold is implemented as a pip package and available at: https://github.com/Qrouger/PPIFold.

More Related Videos

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Related Concept Videos

Protein-protein Interfaces

Protein-protein Interfaces

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...

Protein Networks

Protein Networks

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Folding

Protein Folding

Articles linked to this work by shared authors, journal, and citation graph.

Molecular basis of type VI secretion system effector loading.

Nature microbiology·2026

Dissection and internal anatomy of the giant tropical bont tick Amblyomma variegatum.

Parasite (Paris, France)·2025

Type IV secretion systems: from structures to mechanisms.

The EMBO journal·2025

RQC2 is a major player in peptide release from stalled ribosomes.

Structure (London, England : 1993)·2025

Intricate ribosome composition and translational reprogramming in epithelial-mesenchymal transition.

Proceedings of the National Academy of Sciences of the United States of America·2024

Cryo-EM structure of a conjugative type IV secretion system suggests a molecular switch regulating pilus biogenesis.

The EMBO journal·2024

See all related articles