Publications

2026

23. Li, Z., Wang, S., Sheffler, W., Hsia, Y., Lee, B., Hura, G. L., Yaman, M.Y., Liu, B., Kibler, R.D., Bethel, N.P, .... & Baker, D. (2026). Programmable De Novo Design of Mesoporous Protein Crystal Frameworks. bioRxiv, 2026-08

22. Ma, Z., Herrera, J. E., Bethel, N. P., & Jinich, A. (2026). Inferring Local Protein Structural Similarity from Sequence Alone. JCIM

21. Yu, L. T., Li, X., Pyles, H., Patni, A. P., Borst, A. J., Bethel, N. P., ... & Baker, D. (2026). Templating and confining calcium phosphate mineralization within designed protein assemblies. bioRxiv, 2026-01.

2025

20. Ma, Z. & Bethel, N. (2025). RemoteFoldSet: Benchmarking Structural Awareness of Protein Language Models. bioRxiv

19. Wang, S., Favor, A., Kibler, R. D., Lubner, J. M., Borst, A. J., Coudray, N., ... & Baker, D. (2025). Bond-centric modular design of protein assemblies. Nature Materials, 1-9.

18. Khmelinskaia, A., Bethel, N. P., Fatehi, F., Mallik, B. B., Antanasijevic, A., Borst, A. J., ... & King, N. P. (2025). Local structural flexibility drives oligomorphism in computationally designed protein assemblies. Nature Structural & Molecular Biology, 1-11.

2024

17. Shen, H., Lynch, E. M., Akkineni, S., Watson, J. L., Decarreau, J., Bethel, N. P., ... & Baker, D. (2024). De novo design of pH-responsive self-assembling helical protein filaments. Nature Nanotechnology, 1-6.

16. Huddy, T. F., Hsia, Y., Kibler, R. D., Xu, J., Bethel, N., Nagarajan, D., ... & Baker, D. (2024). Blueprinting extendable nanomaterials with standardized protein blocks. Nature, 627(8005), 898-904.

15. Edman, N. I., Phal, A., Redler, R. L., Schlichthaerle, T., Srivatsan, S. R., Ehnes, D. D., ... & Baker, D. (2024). Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell, 187(14), 3726-3740.

2023

14. Bethel, N. P., Borst, A. J., Parmeggiani, F., Bick, M. J., Brunette, T. J., Nguyen, H., ... & Baker, D. (2023). Precisely patterned nanofibres made from extendable protein multiplexes. Nature Chemistry, 15(12), 1664-1671.

2022

13. Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., ... & Baker, D. (2022). Robust deep learning–based protein sequence design using ProteinMPNN. Science, 378(6615), 49-56.

12. Veling, M. T., Nguyen, D. T., Thadani, N. N., Oster, M. E., Rollins, N. J., Brock, K. P., ... & Silver, P. A. (2022). Natural and designed proteins inspired by extremotolerant organisms can form condensates and attenuate apoptosis in human cells. ACS synthetic biology, 11(3), 1292-1302.

11. Courbet, A., Hansen, J., Hsia, Y., Bethel, N., Park, Y. J., Xu, C., ... & Baker, D. (2022). Computational design of mechanically coupled axle-rotor protein assemblies. Science, 376(6591), 383-390.

2013-2021

10. Han, T. W., Ye, W., Bethel, N. P., Zubia, M., Kim, A., Li, K. H., ... & Jan, L. Y. (2019). Chemically induced vesiculation as a platform for studying TMEM16F activity. Proceedings of the National Academy of Sciences, 116(4), 1309-1318.

9. Argudo, D., Capponi, S., Bethel, N. P., & Grabe, M. (2019). A multiscale model of mechanotransduction by the ankyrin chains of the NOMPC channel. Journal of General Physiology, 151(3), 316-327.

8. Peters, C. J., Gilchrist, J. M., Tien, J., Bethel, N. P., Qi, L., Chen, T., ... & Jan, L. Y. (2018). The sixth transmembrane segment is a major gating component of the TMEM16A calcium-activated chloride channel. Neuron, 97(5), 1063-1077.

7. Argudo, D., Bethel, N. P., Marcoline, F. V., Wolgemuth, C. W., & Grabe, M. (2017). New continuum approaches for determining protein-induced membrane deformations. Biophysical journal, 112(10), 2159-2172.

6. Guerriero, C. J., Reutter, K. R., Augustine, A. A., Preston, G. M., Weiberth, K. F., Mackie, T. D., ... & Brodsky, J. L. (2017). Transmembrane helix hydrophobicity is an energetic barrier during the retrotranslocation of integral membrane ERAD substrates. Molecular biology of the cell, 28(15), 2076-2090.

5. Bethel, N. P., & Grabe, M. (2016). Atomistic insight into lipid translocation by a TMEM16 scramblase. Proceedings of the National Academy of Sciences, 113(49), 14049-14054.

4. Argudo, D., Bethel, N. P., Marcoline, F. V., & Grabe, M. (2016). Continuum descriptions of membranes and their interaction with proteins: towards chemically accurate models. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1858(7), 1619-1634.

3. Marcoline, F. V., Bethel, N., Guerriero, C. J., Brodsky, J. L., & Grabe, M. (2015). Membrane protein properties revealed through data-rich electrostatics calculations. Structure, 23(8), 1526-1537.

2. Hu, M., Cheng, J., Bethel, N., Serra-Hsu, F., Ferreri, S., Lin, L., & Qin, Y. X. (2014). Interrelation between external oscillatory muscle coupling amplitude and in vivo intramedullary pressure related bone adaptation. Bone, 66, 178-181.

1. Hu, M., Serra-Hsu, F., Bethel, N., Lin, L., Ferreri, S., Cheng, J., & Qin, Y. X. (2013). Dynamic hydraulic fluid stimulation regulated intramedullary pressure. Bone, 57(1), 137-141.