Introduction

AlphaFragment: Protein Fragmentation and Pair Generation for AlphaFold and AlphaPulldown

AlphaFragment is a Python package created to improve the preparation of protein data for structural analysis using tools like AlphaFold and AlphaPulldown. The package equips users with efficient methods to import protein data, accurately identify protein domains using information from AlphaFoldDB and UniProt, and perform protein fragmentation while preserving domain integrity. It also facilitates the generation of output files that are immediately ready for structure prediction applications.

Features

AlphaFragment includes:

• Domain Compilation: Efficiently identifies protein domains using a combination of predictions from AlphaFoldDB, information from UniProt and manual input, ensuring accurate domain recognition.

• Protein Fragmentation: Provides tools to fragment proteins according to specified lengths, carefully avoiding disruption of identified domains and regions of interest, and adding overlap between fragments to maximise chances of identifying PPIs.

• Visualization: Includes functionality to generate detailed graphical representations of protein domains and their fragmentation patterns, for easy visual inspection and validation, as well as for use when analysing predictions.

• Output Preparation: Prepares and exports data in formats compatible with AlphaFold and AlphaPulldown.

Getting Started

This documentation is designed to guide you through the installation process and getting started with using AlphaFragment. It also provides detailed information on each class and function included the package.