SUMMARY: AlphaPulldown2 streamlines protein structural modeling by automating workflows, improving code adaptability, and optimizing data management for large-scale applications. It introduces an automated Snakemake pipeline, compressed data storage, support for additional modeling backends like UniFold and AlphaLink2, and a range of other improvements. These upgrades make AlphaPulldown2 a versatile platform for predicting both binary interactions and complex multi-unit assemblies. AVAILABILITY AND IMPLEMENTATION: AlphaPulldown2 is freely available at https://github.com/KosinskiLab/AlphaPulldown.

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.