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Updated: Aug 20, 2025

Pulldown Assay Coupled with Co-Expression in Bacteria Cells as a Time-Efficient Tool for Testing Challenging Protein-Protein Interactions
Published on: December 23, 2022
AlphaPulldown-a python package for protein-protein interaction screens using AlphaFold-Multimer
Dingquan Yu1,2, Grzegorz Chojnowski1, Maria Rosenthal3
1European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany.
Summary:
The artificial intelligence-based structure prediction program AlphaFold-Multimer enabled structural modelling of protein complexes with unprecedented accuracy. Increasingly, AlphaFold-Multimer is also used to discover new protein-protein interactions (PPIs). Here, we present AlphaPulldown, a Python package that streamlines PPI screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command-line interface, a variety of confidence scores and a graphical analysis tool.
Availability And Implementation:
AlphaPulldown is freely available at https://www.embl-hamburg.de/AlphaPulldown.
Supplementary Information:
Supplementary note is available at Bioinformatics online.
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