AlphaPulldown2 – A General Pipeline for High-Throughput Structural Modeling

  1. Dmitry Molodenskiy
  2. Valentin J. Maurer
  3. Dingquan Yu
  4. Grzegorz Chojnowski
  5. Stefan Bienert
  6. Gerardo Tauriello
  7. Konstantin Gilep
  8. Torsten Schwede
  9. Jan Kosinski
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Abstract

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

AlphaPulldown2 is freely available at<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/KosinskiLab/AlphaPulldown">https://github.com/KosinskiLab/AlphaPulldown</ext-link>.

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