AlphaPulldown—a Python Package for Protein–protein Interaction Screens Using AlphaFold-Multimer

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. Here, we present AlphaPulldown , a Python package that streamlines protein-protein interaction 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 .