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Real-Time Structure Search and Structure Classification for AlphaFold Protein Models
Open accessPreprint — published as 10.1038/s42003-022-03261-8 · Paper page
Abstract
AlphaFold2 showed a substantial improvement in the accuracy of protein structure prediction. Following the release of the software, whole-proteome protein structure predictions by AlphaFold2 for 21 organisms were made publicly available. Here, we developed the infrastructure, 3D-AF-Surfer, to enable real-time structure-based search for the AlphaFold2 models by combining molecular surface representation with 3D Zernike descriptors and deep neural networks.
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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
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Metadata
- Authors
- Aderinwale, T., Bharadwaj, V., Christoffer, C., Terashi, G., Zhang, Z., Jahandideh, R., Kagaya, Y., & Kihara, D.
- Affiliations
- Purdue University West Lafayette (US)
- Corresponding author
- Kihara, Daisuke
- Venue
- Communications Biology
- Publisher
- openRxiv
- Published
- 2021-10-23
- Volume
- 5
- Issue
- 1
- Pages
- 316-316
- ISSN
- 2399-3642 (ISSN-L)
- PMC
- PMC8983703
- OpenAlex
- W4226320411
- Cited by
- 61
- References
- 1
- Citations by year
- 2026: 5 · 2025: 9 · 2024: 18 · 2023: 14 · 2022: 15
- FWCI
- 4.57
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Communications Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Science Foundation (1925643, 2003635, 1825941)
- U.S. Department of Health and Human Services (3R01 GM133840-02S1, R01GM133840, R01GM123055)
- National Institutes of Health (CMMI1825941)
- Directorate for Engineering (CMMI1825941)
- National Institute of General Medical Sciences (R01GM123055, R01GM133840, T32GM132024)
- Division of Civil, Mechanical and Manufacturing Innovation (CMMI1825941)
- Division of Molecular and Cellular Biosciences (MCB1925643)
- Division of Biological Infrastructure (DBI2003635)
- 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 › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- AlphaFold2, protein structure prediction, structural classification, neural network retrieval, protein folding
- MeSH terms
- Models, Molecular, Proteins, Software, Neural Networks, Computer
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