AlphaPulldown

Description

alphapulldown website

AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer: * provides a convenient command line interface to screen a bait protein against many candidates, calculate all-versus-all pairwise comparisons, test alternative homo-oligomeric states, and model various parts of a larger complex * separates the CPU stages (MSA and template feature generation) from GPU stages (the actual modeling) * allows modeling fragments of proteins without recalculation of MSAs and keeping the original full-length residue numbering in the models * summarizes the results in a CSV table with AlphaFold scores, pDockQ and mpDockQ, PI-score, and various physical parameters of the interface * provides a Jupyter notebook for an interactive analysis of PAE plots and models

Environment Modules

Run module spider alphapulldown to find out what environment modules are available for this application.

Environment Variables

• HPC_ALPHAPULLDOWN_DIR - installation directory
• HPC_ALPHAPULLDOWN_BIN - executable directory NOTE: AlphaFold databses located under $HPC_ALPHAFOLD_REF

Citation

If you use this software, please cite it along the dependencies it uses internally, at least:

Yu,D. et al. (2022) AlphaPulldown – a Python package for protein-protein interaction screens using AlphaFold-Multimer. Bioinformatics, Volume 39, Issue 1, January 2023, btac749

Jumper,J. et al. (2021) Highly accurate protein structure prediction with AlphaFold. Nature 2021 596:7873, 596, 583–589.

Evans,R. et al. (2022) Protein complex prediction with AlphaFold-Multimer.

Categories

protein, structure, machine_learning