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.
© The Author(s) 2022. Published by Oxford University Press.