AlphaPulldown2-a general pipeline for high-throughput structural modeling.

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Dmitry Molodenskiy, Valentin J Maurer, Dingquan Yu, Grzegorz Chojnowski, Stefan Bienert, Gerardo Tauriello, Konstantin Gilep, Torsten Schwede, Jan Kosinski

Author Information

Dmitry Molodenskiy: European Molecular Biology Laboratory Hamburg, Hamburg, 22607, Germany.
Valentin J Maurer: European Molecular Biology Laboratory Hamburg, Hamburg, 22607, Germany.
Dingquan Yu: European Molecular Biology Laboratory Hamburg, Hamburg, 22607, Germany.
Grzegorz Chojnowski: European Molecular Biology Laboratory Hamburg, Hamburg, 22607, Germany.
Stefan Bienert: Biozentrum, University of Basel, Basel, Switzerland.
Gerardo Tauriello: Biozentrum, University of Basel, Basel, Switzerland.
Konstantin Gilep: European Molecular Biology Laboratory Hamburg, Hamburg, 22607, Germany.
Torsten Schwede: Biozentrum, University of Basel, Basel, Switzerland.
Jan Kosinski: European Molecular Biology Laboratory Hamburg, Hamburg, 22607, Germany.

PMID: 40088942 DOI: 10.1093/bioinformatics/btaf115

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.
SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

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