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Utilizing artificial intelligence system to build the digital structural proteome of reef-building corals
Open accessPreprint — published as 10.1093/gigascience/giac117
Abstract
Reef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals. 8,382 proteins co-expressed in A. muricata, M. foliosa and P. verrucosa were identified, then 8,166 of them got predicted structures after around 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence. Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.
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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
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Metadata
- Authors
- Zhu, Y., Liao, X., Han, T., Chen, J.-Y., He, C., & Lu, Z.
- Affiliations
- State Key Laboratory of Digital Medical Engineering (CN)
- Guangxi Mangrove Research Center (CN)
- Chinese Academy of Sciences (CN)
- Corresponding author
- He, Chunpeng
- Lu, Zuhong
- Venue
- GigaScience
- Publisher
- openRxiv
- Published
- 2022-06-30
- Volume
- 11
- ISSN
- 2047-217X (ISSN-L)
- PMC
- PMC9673494
- OpenAlex
- W4309665402
- Cited by
- 4
- References
- 1
- Citations by year
- 2024: 2 · 2023: 1 · 2022: 1
- FWCI
- 0.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- GigaScience (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Southeast University (Sklb2021-k02)
- State Key Laboratory of Bioelectronics (Sklb2021-k02)
- Guangxi Key Laboratory of Mangrove Conservation and Utilization (GKLMC-202002)
- Open Research Fund of State Key Laboratory of Bioelectronics
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Environmental Science › Ecology › Coral and Marine Ecosystems Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- reef-building corals, protein structure prediction, ColabFold, Acropora muricata, Pocillopora verrucosa, homologous proteins, mass spectrometry, GPU computing, structural proteomics
- MeSH terms
- Animals, Artificial Intelligence, Reproducibility of Results, Ecosystem, Proteome, Anthozoa, Coral Reefs
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