Hsia, Y. et al. Design of a hyperstable 60-subunit protein icosahedron. Nature 535, 136–139 (2016).
Caspar, D. L. D. & Klug, A. Physical principles in the construction of regular viruses. Cold Spring Harb. Symp. Quant. Biol. 27, 1–24 (1962).
Rayment, I., Baker, T. S., Caspar, D. L. D. & Murakami, W. T. Polyoma virus capsid structure at 22.5 Å resolution. Nature 295, 110–115 (1982).
Liddington, R. C. et al. Structure of simian virus 40 at 3.8-Å resolution. Nature 354, 278–284 (1991).
Prasad, B. V. V. et al. X-ray crystallographic structure of the Norwalk virus capsid. Science 286, 287–290 (1999).
Abad-Zapatero, C. et al. Structure of southern bean mosaic virus at 2.8 Å resolution. Nature 286, 33–39 (1980).
Harrison, S. C., Olson, A. J., Schutt, C. E., Winkler, F. K. & Bricogne, G. Tomato bushy stunt virus at 2.9 Å resolution. Nature 276, 368–373 (1978).
Lee, S. et al. Four-component protein nanocages designed by programmed symmetry breaking. Nature 638, 546–552 (2025).
Dowling, Q. M. et al. Hierarchical design of pseudosymmetric protein nanocages. Nature 638, 553–561 (2025).
Xia, X. et al. RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells. Cell 187, 2236–2249 (2024).
Wagner, J. & Zandi, R. The robust assembly of small symmetric nanoshells. Biophys. J. 109, 956–965 (2015).
Li, S., Roy, P., Travesset, A. & Zandi, R. Why large icosahedral viruses need scaffolding proteins. Proc. Natl Acad. Sci. USA 115, 10971–10976 (2018).
Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023).
Dauparas, J. et al. Robust deep learning–based protein sequence design using ProteinMPNN. Science 378, 49–56 (2022).
Chen, D.-H. et al. Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc. Natl Acad. Sci. USA 108, 1355–1360 (2011).
Chmielewski, D., Schmid, M. F., Simmons, G., Jin, J. & Chiu, W. Chikungunya virus assembly and budding visualized in situ using cryogenic electron tomography. Nat. Microbiol. 7, 1270–1279 (2022).
Dai, X. et al. In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus. Nature 541, 112–116 (2017).
Ilca, S. L. et al. Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat. Commun. 6, 8843 (2015).
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta. Cryst. D Struct. Biol. 74, 519–530 (2018).
Khmelinskaia, A. et al. Local structural flexibility drives oligomorphism in computationally designed protein assemblies. Nat. Struct. Mol. Biol. 32, 1050–1060 (2025).
Zhao, G. et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497, 643–646 (2013).
Levandovsky, A. & Zandi, R. Nonequilibirum assembly, retroviruses, and conical structures. Phys. Rev. Lett. 102, 198102 (2009).
Walsh, M. R., Koh, C. A., Sloan, E. D., Sum, A. K. & Wu, D. T. Microsecond simulations of spontaneous methane hydrate nucleation and growth. Science 326, 1095–1098 (2009).
Lin, H. et al. Clathrate colloidal crystals. Science 355, 931–935 (2017).
Frank, F. C. & Kasper, J. S. Complex alloy structures regarded as sphere packings. I. Definitions and basic principles. Acta Crystallogr. 11, 184–190 (1958).
Morris, K. L. et al. Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly. Nat. Struct. Mol. Biol. 26, 890–898 (2019).
Wang, S. et al. De novo design of quasisymmetric two-component protein cages. Nature https://doi.org/10.1038/s41586-026-10464-0 (2026).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Anderson, J. A., Glaser, J. & Glotzer, S. C. HOOMD-blue: a Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations. Comput. Mater. Sci. 173, 109363 (2020).
Kibler, R. D. et al. Design of pseudosymmetric protein hetero-oligomers. Nat. Commun. 15, 10684 (2024).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
Hagen, W. J. H., Wan, W. & Briggs, J. A. G. Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J. Struct. Biol. 197, 191–198 (2017).
Chen, M. et al. A complete data processing workflow for cryo-ET and subtomogram averaging. Nat. Methods 16, 1161–1168 (2019).

