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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., Chojnowski, G., Rosenthal, M., & Kosinski, J. (2022). AlphaPulldown – a Python package for protein–protein interaction screens using AlphaFold-Multimer. Bioinformatics, 39(1), btac749. https://doi.org/10.1093/bioinformatics/btac749

Jumper, J., Evans, R., Pritzel, A., et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583–589. https://doi.org/10.1038/s41586-021-03819-2

Evans, R., O’Neill, M., Pritzel, A., et al. (2022). Protein complex prediction with AlphaFold-Multimer. bioRxiv. https://doi.org/10.1101/2021.10.04.463034

Categories

protein, structure, machine_learning