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Conditioned Protein Structure Prediction
Open accessPreprint — published as 10.1103/prxlife.2.043001
Abstract
Deep learning based protein structure prediction has facilitated major breakthroughs in biological sciences. However, current methods struggle with alternative conformation prediction and offer limited integration of expert knowledge on protein dynamics. We introduce AFEXplorer, a generic approach that tailors AlphaFold predictions to user-defined constraints in coarse coordinate spaces by optimizing embedding features. Its effectiveness in generating functional protein conformations in accordance with predefined conditions were demonstrated through comprehensive examples. AFEXplorer serves as a versatile platform for conditioned protein structure prediction, bridging the gap between automated models and domain-specific insights.
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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
Sampling alternative conformational states of transporters and receptors with AlphaFold2
del Alamo, D., Sala, D., Mchaourab, H. S., & Meiler, J. (2022) · eLife · doi:10.7554/elife.75751 · Cited by 511
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Metadata
- Authors
- Xie, T., Song, Z., & Huang, J.
- Affiliations
- Westlake University (CN)
- Corresponding author
- Huang, Jing
- Venue
- PRX Life
- Publisher
- openRxiv
- Published
- 2023-09-25
- Volume
- 2
- Issue
- 4
- ISSN
- 2835-8279 (ISSN-L)
- OpenAlex
- W4403130667
- Cited by
- 16
- References
- 2
- Citations by year
- 2026: 9 · 2025: 3 · 2024: 4
- FWCI
- 2.18
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Licence
- cc-by
- Locations
- PRX Life (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- Funders
- Westlake University
- National Natural Science Foundation of China (32171247, 21803057)
- 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 structure prediction, AlphaFold, embedding optimization, protein dynamics, expert knowledge integration
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