The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
SPIRED-Fitness: an end-to-end framework for the prediction of protein structure and fitness from single sequence
Open accessPreprint — published as 10.1038/s41467-024-51776-x · Paper page
Abstract
Significant research progress has been made in the field of protein structure and fitness prediction. Particularly, single-sequence-based structure prediction methods like ESMFold and OmegaFold achieve a balance between inference speed and prediction accuracy, showing promise for many downstream prediction tasks. Here, we propose SPIRED, a novel single-sequence-based structure prediction model that exhibits comparable performance to the state-of-the-art methods but with approximately 5-fold acceleration in inference and at least one order of magnitude reduction in training consumption. By integrating SPIRED with downstream neural networks, we compose an end-toend framework named SPIRED-Fitness for the rapid prediction of both protein structure and fitness from single sequence. SPIRED-Fitness and its derivative SPIRED-Stab achieve state-of-the-art performance in predicting the mutational effects on protein fitness and stability metrics, respectively.
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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
A structural biology community assessment of AlphaFold2 applications
Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00849-w · Cited by 675
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Metadata
- Authors
- Gong, H., Chen, Y., Xu, Y., Liu, D., & Xing, Y.
- Affiliations
- Tsinghua University (CN)
- Tsinghua University
- Corresponding author
- Gong, Haipeng
- Venue
- Nature Communications
- Published
- 2024-03-07
- Volume
- 15
- Issue
- 1
- Pages
- 7400-7400
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC11349999
- OpenAlex
- W4401900858
- Cited by
- 45
- References
- 2
- Citations by year
- 2026: 17 · 2025: 24 · 2024: 4
- FWCI
- 6.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Natural Science Foundation of China (32171243)
- Ministry of Science and Technology of the People's Republic of China (2023YFF1204400)
- 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, protein fitness prediction, end-to-end framework, inference acceleration, protein engineering, ESMFold
- MeSH terms
- Algorithms, Models, Molecular, Mutation, Protein Conformation, Proteins, Neural Networks, Computer, Computational Biology, Sequence Analysis, Protein, Protein Stability
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