# PPIFold: a tool for analysis of protein–protein interaction from AlphaPullDown

## TL;DR

PPIFold is a new tool that simplifies the analysis of protein–protein interactions by automating complex steps, making it more accessible for researchers.

## Contribution

PPIFold introduces an automated pipeline for PPI analysis, streamlining pre- and post-processing tasks.

## Key findings

- PPIFold was validated on a bacterial Type 4 Secretion System, showing its effectiveness.
- The tool enhances accessibility and simplifies PPI prediction interpretation for researchers.

## Abstract

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.

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.

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