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AlphaPulldown2 – A General Pipeline for High-Throughput Structural Modeling
Open accessPreprint — published as 10.1093/bioinformatics/btaf115 · Paper page
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 https://github.com/KosinskiLab/AlphaPulldown .
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07487-w · Cited by 15,861
Ahdritz, G., Bouatta, N., Floristean, C., Kadyan, S., Xia, Q., Gerecke, W., O’Donnell, T. J., Berenberg, D., Fisk, I., Zanichelli, N., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02272-z · Cited by 439
Towards a structurally resolved human protein interaction network
Burke, D. F., Bryant, P., Barrio-Hernandez, I., Memon, D., Pozzati, G., Shenoy, A., Zhu, W., Dunham, A. S., Albanese, P., Keller, A., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00910-8 · Cited by 269
High-throughput prediction of protein conformational distributions with subsampled AlphaFold2
Monteiro da Silva, G., Cui, J. Y., Dalgarno, D. C., Lisi, G. P., & Rubenstein, B. M. (2024) · Nature Communications · doi:10.1038/s41467-024-46715-9 · Cited by 196
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Metadata
- 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)
- ORCID
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2024-12-03
- OpenAlex
- W4404945890
- Cited by
- 0
- References
- 5
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- Desy publication database (The Deutsches Elektronen-Synchrotron) (submittedVersion, other-oa)
- Funders
- Deutsche Forschungsgemeinschaft
- Swiss Institute of Bioinformatics
- HORIZON EUROPE European Research Council (101119142)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- protein structure modeling, Snakemake, protein-protein interaction, AlphaFold
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