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High-resolution real-space reconstruction of cryo-EM structures using a neural field network
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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
Fourier Features Let Networks Learn High Frequency Functions in Low Dimensional Domains
Tancik, M., Srinivasan, P. P., Mildenhall, B., Fridovich-Keil, S., Raghavan, N., Singhal, U., Ramamoorthi, R., Barron, J. T., & Ng, R. (2020) · arXiv · doi:10.48550/arxiv.2006.10739 · Cited by 1,459
Research works printed but not linked: 37
- Smith, M. T. J. & Rubinstein, J. L. Beyond blob-ology. Science 345, 617–619 (2014). · DOI
- Renaud, J. P. et al. Cryo-EM in drug discovery: achievements, limitations and prospects. Nat. Rev. Drug Discov. 17, 471–492 (2018). · DOI
- Terwilliger, T. C. et al. AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination. Nat. Methods 21, 110–116 (2023). · DOI · Paper page
- Yang, Z. et al. AlphaFold2 and its applications in the fields of biology and medicine. Sig. Transduct. Target. Ther. 8, 115 (2023). · DOI
- Nogales, E. The development of cryo-EM into a mainstream structural biology technique. Nat. Methods 13, 24–27 (2016). · DOI
- Cheng, Y. Single-particle cryo-EM at crystallographic resolution. Cell 161, 450–457 (2015). · DOI
- Zhou, X. et al. Progressive assembly of multi-domain protein structures from cryo-EM density maps. Nat. Comput. Sci. 2, 265–275 (2022). · DOI · Paper page
- Zhang, Z. et al. DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. Brief. Bioinform. 25, bbae113 (2024). · DOI
- Bendory, T., Bartesaghi, A. & Singer, A. Single-particle cryo-electron microscopy: mathematical theory, computational challenges, and opportunities. IEEE Signal Process. Magazine 37, 58–76 (2020). · DOI
- Singer, A. & Sigworth, F. J. Computational methods for single-particle electron cryomicroscopy. Annu. Rev. Biomed. Data Sci. 3, 163–190 (2020). · DOI
- Namba, K. & Makino, F. Recent progress and future perspective of electron cryomicroscopy for structural life sciences. Microscopy 71, i3–i14 (2022). · DOI
- Nakane, T. et al. Single-particle cryo-EM at atomic resolution. Nature 587, 152–156 (2020). · DOI
- Yip, K. M. et al. Atomic-resolution protein structure determination by cryo-EM. Nature 587, 157–161 (2020). · DOI
- Scheres, S. H. W. A Bayesian view on cryo-EM structure determination. J. Mol. Biol. 415, 406–418 (2012). · DOI
- Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012). · DOI · Paper page
- Punjani, A. et al. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). · DOI · Paper page
- Grant, T., Rohou, A. & Grigorieff, N. cisTEM, user-friendly software for single-particle image processing. eLife 7, e35383 (2018). · DOI
- Wang, G., Ye, J. C. & De Man, B. Deep learning for tomographic image reconstruction. Nat. Mach. Intell. 2, 737–748 (2020). · DOI · Paper page
- Zhong, E. D. et al. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat. Methods 18, 176–185 (2021). · DOI
- Chen, M. & Ludtke, S. J. Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM. Nat. Methods 18, 930–936 (2021). · DOI
- Punjani, A. & Fleet, D. J. 3DFlex: determining structure and motion of flexible proteins from cryo-EM. Nat. Methods 20, 860–870 (2023) · DOI
- Mildenhall, B. et al. NeRF: representing scenes as neural radiance fields for view synthesis. Commun. ACM 65, 99–106 (2021). · DOI · Paper page
- Liao, M. et al. Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504, 107–112 (2013). · DOI
- Davis, J. H. et al. Modular assembly of the bacterial large ribosomal subunit. Cell 167, 1610–1622.e15 (2016). · DOI
- Ru, H. et al. Molecular mechanism of V(D)J recombination from synaptic RAG1-RAG2 complex structures. Cell 163, 1138–1152 (2015). · DOI
- Ke, Z. et al. Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature 588, 498–502 (2020). · DOI
- Leschziner, A. E. & Nogales, E. Visualizing flexibility at molecular resolution: analysis of heterogeneity in single-particle electron microscopy reconstructions. Annu. Rev. Biophys. Biomol. Struct. 36, 43–62 (2007). · DOI
- Bai, X. C., McMullan, G. & Scheres, S. H. W. How cryo-EM is revolutionizing structural biology. Trends Biochem. Sci. 40, 49–57 (2015). · DOI
- Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017). · DOI
- Levy, A. et al. CryoAI: amortized inference of poses for ab initio reconstruction of 3D molecular volumes from real cryo-EM images. In Computer Vision—ECCV 2022 540–557 (Springer, 2022). · DOI
- Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020). · DOI
- Terwilliger, T. C. et al. Improvement of cryo-EM maps by density modification. Nat. Methods 17, 923–927 (2020). · DOI
- Terwilliger, T. C. et al. Density modification of cryo-EM maps. Acta Cryst. D76, 912–925 (2020).
- Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Cryst. D75, 861–877 (2019).
- Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014). · DOI
- Kingma, D. P. & Welling, M. Auto-encoding variational Bayes. In 2nd International Conference on Learning Representations (ICLR, 2014).
- Iudin, A. et al. EMPIAR: the Electron Microscopy Public Image Archive. Nucleic Acids Res. 51, D1503–D1511 (2023). · DOI
Metadata
- Authors
- Huang, Y., Zhu, C., Yang, X., & Liu, M.
- Affiliations
- Shanghai Jiao Tong University (CN)
- Corresponding author
- Yang, Xiaokang
- Liu, Manhua
- Venue
- Nature Machine Intelligence
- Published
- 2024-07-12
- Volume
- 6
- Issue
- 8
- Pages
- 892-903
- ISSN
- 2522-5839 (ISSN-L)
- OpenAlex
- W4400588667
- Cited by
- 9
- References
- 2
- Citations by year
- 2026: 4 · 2025: 5
- FWCI
- 1.65
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Machine Intelligence (publishedVersion)
- Research Square (acceptedVersion, cc-by)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- 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
- Keywords
- SARS-CoV-2, high-resolution structure determination
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- Huang, Y., Zhu, C., Yang, X., & Liu, M. (2024). High-resolution real-space reconstruction of cryo-EM structures using a neural field network. Nature Machine Intelligence. https://doi.org/10.1038/s42256-024-00870-2