AlphaPulldown2—a general pipeline for high-throughput structural modeling
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Abstract
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.
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Cites
Highly accurate protein structure prediction with AlphaFold
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Accurate structure prediction of biomolecular interactions with AlphaFold 3
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UniProt: the Universal Protein Knowledgebase in 2023
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bye-A-Jee, H., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1052 · Cited by 7,210 · see citing works
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“We plan to incorporate additional modeling backends, including OpenFold.”
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- Authors
- Molodenskiy, D., Maurer, V. J., Yu, D., Chojnowski, G., Bienert, S., Tauriello, G., Gilep, K., Schwede, T., & Kosinski, J.
- Affiliations
- European Molecular Biology Laboratory (DE)
- SIB Swiss Institute of Bioinformatics (CH)
- European Molecular Biology Laboratory Hamburg , Hamburg 22607,
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2025-03
- Volume
- 41
- Issue
- 3
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC11937959
- OpenAlex
- W4408503115
- Cited by
- 15
- References
- 7
- Citations by year
- 2026: 12 · 2025: 3
- FWCI
- 4.48
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- German Research Foundation (KO 5979/2)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein structure modeling, Snakemake, AlphaFold, data compression
- MeSH terms
- Models, Molecular, Protein Conformation, Proteins, Software, Computational Biology
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