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AlphaPulldown – a Python package for protein-protein interaction screens using AlphaFold-Multimer
Open accessPreprint — published as 10.1093/bioinformatics/btac749 · Paper page
Abstract
Summary: The Artificial Intelligence-based structure prediction program AlphaFold-Multimer enabled structural modelling of protein complexes with unprecedented accuracy. Increasingly, AlphaFold-Multimer is also used to discover new protein-protein interactions. Here, we present AlphaPulldown , a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command line interface, a variety of confidence scores, and a graphical analysis tool. Availability and implementation: AlphaPulldown is freely available at https://www.embl-hamburg.de/AlphaPulldown .
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References 8 · Cited by 17
Research works printed but not linked: 6
- Bryant, P. , Pozzati, G. , Zhu, W. , et al. (2022) Predicting the structure of large protein complexes using AlphaFold and sequential assembly. bioRxiv, 2022.03.12.484089. · DOI · Paper page
- Evans, R. et al. (2022) Protein complex prediction with AlphaFold-Multimer. · DOI · Paper page
- Humphreys, I. et al. (2021) Computed structures of core eukaryotic protein complexes. Science (1979), 374. · DOI · Paper page
- 2021, Assessment of protein–protein interfaces in cryo-EM derived assemblies, Nature Communications 2021 12:1, 12, 1
- 2022, ColabFold: making protein folding accessible to all, Nature Methods 2022 19:6, 19, 679
- Mosalaganti, S. et al. (2022) AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science (1979), 376. · DOI · Paper page
Metadata
- Authors
- Yu, D., Chojnowski, G., Rosenthal, M., & Kosinski, J.
- Affiliations
- European Molecular Biology Laboratory (DE)
- Bernhard Nocht Institute for Tropical Medicine (DE)
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2022-08-06
- OpenAlex
- W4290473117
- Cited by
- 17
- References
- 8
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 8 · 2023: 6
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Desy Publications Database (Deutsches Elektronen-Synchrotron DESY) (submittedVersion, cc-by)
- Funders
- Deutsche Forschungsgemeinschaft
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- protein-protein interaction, AlphaFold-Multimer, protein complex structure prediction, oligomerization, confidence scores, command-line interface, graphical analysis tool
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