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Essays

Vol. 158 No. 2 (2025): Rendiconti. Mathematics and Natural Sciences Class

Structural biology and artificial intelligence: a multidisciplinary revolution in understanding protein structures

  • Federico Forneris
DOI
https://doi.org/10.3280/rndoa2025oa21153
Submitted
ottobre 1, 2025
Published
2026-02-17

Abstract

Structural biology is a fascinating and constantly evolving discipline that focuses on studying the three-dimensional structure of biological macromolecules and their relationship with cellular functions. Through advanced experimental and computational techniques, researchers progressively gain a deeper understanding of the molecular mechanisms that govern life. This knowledge has direct implications for human health by shedding light on the molecular basis of various diseases, opening up innovative perspectives for the development of targeted and effective drugs. The following presentation aims to provide an introduction to structural biology, with particular emphasis on the problem of protein folding and the revolutionary impact that artificial intelligence has had in this field in recent years. In relation to this topic, and to highlight how AI-based tools can serve as a valuable resource for scientific research when used appropriately, I would like to clarify that I have utilized artificial intelligence tools in drafting this text. Specifically, the first draft of this presentation was generated by the ChatGPT software based on the transcription of a talk given at the Lombard Institute. This transcription was also obtained using artificial intelligence by analyzing the recording of the talk available on YouTube through the Panopto software.

References

  1. Bai X.C., Gonen T., Gronenborn A.M., Perrakis A., Thorn A. and Yang J. (2024). Challenges and opportunities in macromolecular structure determination. In: «Nat Rev Mol Cell Biol», 25: 7-12. Doi: 10.1038/s41580-023-00659-y.
  2. Bai X.C., McMullan G. and Scheres S.H. (2015). How cryo-EM is revolutionizing structural biology. In: «Trends Biochem Sci», 40: 49-57. Doi: 10.1016/j.tibs.2014.10.005.
  3. Berman H., Henrick K. and Nakamura H. (2003). Announcing the worldwide Protein Data Bank. In: «Nat Struct Biol», 10: 980. Doi: 10.1038/nsb1203-980.
  4. Eisenberg D. (2003). The discovery of the α-helix and β-sheet, the principal structural features of proteins. In: «Proceedings of the National Academy of Sciences», 100: 11207-11210. Doi: 10.1073/pnas.2034522100.
  5. Elofsson A. (2023). Progress at protein structure prediction, as seen in CASP15. In: «Curr Opin Struct Biol», 80: 102594. Doi: 10.1016/j.sbi.2023.102594.
  6. Fitzpatrick A.W.P., Falcon B., He S., Murzin A.G., Murshudov G., Garringer H.J., Crowther R.A., Ghetti B., Goedert M. and Scheres S.H.W (2017). Cryo-EM structures of tau filaments from Alzheimer’s disease. In: «Nature», 547: 185-190. Doi: 10.1038/nature23002.
  7. Heck A.J. (2008). Native mass spectrometry: a bridge between interactomics and structural biology. In: «Nat Methods», 5: 927-933. Doi: 10.1038/nmeth.1265.
  8. Humphreys I.R., Pei J., Baek M., Krishnakumar A., Anishchenko I., Ovchinnikov S., Zhang J., Ness T.J., Banjade S., Bagde S.R., Stancheva V.G., Li X.H., Liu K., Zheng Z., Barrero D.J., Roy U., Kuper J., Fernandez I.S., Szakal B., Branzei D., Rizo J., Kisker C., Greene E.C., Biggins S., Keeney S., Miller E.A., Fromme J.C., Hendrickson T.L., Cong Q. and Baker D. (2021). Computed structures of core eukaryotic protein complexes. In: «Science», 374: eabm4805. Doi: 10.1126/science.abm4805.
  9. Iacobucci C., Gotze M. and Sinz A. (2019). Cross-linking/mass spectrometry to get a closer view on protein interaction networks. In: «Curr Opin Biotechnol», 63: 48-53. Doi: 10.1016/j.copbio.2019.12.009.
  10. Jumper J., Evans R., Pritzel A., Green T., Figurnov M., Ronneberger O., Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A, Meyer C, Kohl S.A.A., Ballard A.J., Cowie A., Romera-Paredes B., Nikolov S., Jain R., Adler J., Back T., Petersen S., Reiman D., Clancy E., Zielinski M., Steinegger M., Pacholska M., Berghammer T., Bodenstein S., Silver D., Vinyals O., Senior A.W., Kavukcuoglu K., Kohli P. and Hassabis D. (2021). Highly accurate protein structure prediction with AlphaFold. In: «Nature», 596: 583-589. Doi: 10.1038/s41586-021-03819-2.
  11. Kryshtafovych A., Schwede T., Topf M., Fidelis K. and Moult J. (2021). Critical assessment of methods of protein structure prediction (CASP)-Round XIV. In: «Proteins», 89: 1607-1617. Doi: 10.1002/prot.26237.
  12. Kuhlbrandt W. (2014). Cryo-EM enters a new era. In: «elife», 3: e03678. Doi: 10.7554/eLife.03678.
  13. Levinthal C. (1968). Are there pathways for protein folding?. In: «J. Chim. Phys.» 65: 44-45. Doi: 10.1051/jcp/1968650044.
  14. Id. (1969). How to fold graciously. In: Mössbaun spectroscopy in biological systems proceedings. Univ. of Illinois Bulletin. Champaign: University of Illinois Press, 22-26.
  15. Mahamid J., Pfeffer S., Schaffer M., Villa E., Danev R., Cuellar L.K., Forster F., Hyman A.A., Plitzko J.M. and Baumeister W. (2016). Visualizing the molecular sociology at the HeLa cell nuclear periphery. In: «Science», 351: 969-972. Doi: 10.1126/science.aad8857.
  16. Marion D. (2013). An Introduction to biological NMR spectroscopy. In: «Molecular & Cellular Proteomics», 12: 3006-3025. Doi: 10.1074/mcp.O113.030239.
  17. Maritan M., Autin L., Karr J., Covert M.W., Olson A.J. and Goodsell D.S. (2022). Building structural models of a whole mycoplasma cell. In: «J Mol Biol», 434: 167351. Doi: 10.1016/j.jmb.2021.167351.
  18. Morris G.M. and Lim-Wilby M. (2008). Molecular docking. In: «Methods Mol Biol», 443: 365-382. Doi: 10.1007/978-1-59745-177-2_19.
  19. Oikonomou C.M. and Jensen G.J. (2017). Cellular electron cryotomography: toward structural biology in situ. In: «Annu Rev Biochem», 86: 873-896. Doi: 10.1146/annurev-biochem-061516-044741.
  20. Regan L., Caballero D., Hinrichsen M.R., Virrueta A., Williams D.M. and O’Hern C.S. (2015). Protein design: past, present, and future. In: «Biopolymers», 104: 334-350. Doi: 10.1002/bip.22639.
  21. Strandberg B. (2009). Chapter 1: building the ground for the first two protein structures: myoglobin and haemoglobin. In: «J Mol Biol» 392: 2-10. Doi: 10.1016/j.jmb.2009.05.087.
  22. Thompson B. and Petric Howe N. (2024). Alphafold 3.0: the AI protein predictor gets an upgrade. In: «Nature». Doi: 10.1038/d41586-024-01385-x.
  23. Thorn A. (2022). Artificial intelligence in the experimental determination and prediction of macromolecular structures. In: «Curr Opin Struct Biol», 74: 102368. Doi: 10.1016/j.sbi.2022.102368.
  24. Tunyasuvunakool K., Adler J., Wu Z., Green T., Zielinski M., Zidek A., Bridgland A., Cowie A., Meyer C., Laydon A., Velankar S., Kleywegt G.J., Bateman A., Evans R., Pritzel A., Figurnov M., Ronneberger O., Bates R., Kohl S.A.A., Potapenko A., Ballard A.J., Romera-Paredes B., Nikolov S., Jain R., Clancy E., Reiman D., Petersen S., Senior A.W., Kavukcuoglu K., Birney E., Kohli P., Jumper J. and Hassabis D. (2021). Highly accurate protein structure prediction for the human proteome. In: «Nature», 596: 590-596. Doi: 10.1038/s41586-021-03828-1.
  25. van den Hoek H., Klena N., Jordan M.A., Alvarez Viar G., Righetto R.D., Schaffer M., Erdmann P.S., Wan W., Geimer S., Plitzko J.M., Baumeister W., Pigino G., Hamel V., Guichard P. and Engel B.D. (2022). In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains. In: «Science», 377: 543-548. Doi: 10.1126/science.abm6704.
  26. Varadi M., Anyango S., Deshpande M., Nair S., Natassia C., Yordanova G., Yuan D., Stroe O., Wood G., Laydon A., Zidek A., Green T., Tunyasuvunakool K., Petersen S., Jumper J., Clancy E., Green R., Vora A., Lutfi M., Figurnov M., Cowie A., Hobbs N., Kohli P., Kleywegt G., Birney E., Hassabis D and Velankar S. (2022). AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. In: «Nucleic Acids Res», 50: D439-D444. Doi: 10.1093/nar/gkab1061.
  27. Wohlwend J., Corso G., Passaro S., Reveiz M., Leidal K., Swiderski W., Portnoi T., Chinn I., Silterra J., Jaakkola T. and Barzilay R. (2024). Boltz-1 democratizing biomolecular interaction modeling. In: bioRxiv. Doi: 10.1101/2024.11.19.624167.
  28. Wu M. and Lander G.C. (2020). How low can we go? Structure determination of small biological complexes using single-particle cryo-EM. In: «Curr Opin Struct Biol», 64: 9-16. Doi: 10.1016/j.sbi.2020.05.007.
  29. Yan X. and Maier C.S. (2009). Hydrogen/deuterium exchange mass spectrometry. In: «Methods Mol Biol», 492: 255-271. Doi: 10.1007/978-1-59745-493-3_15.
  30. Yang Y., Arseni D., Zhang W., Huang M., Lövestam S., Schweighauser M., Kotecha A., Murzin A.G., Peak-Chew S.Y., Macdonald J., Lavenir I., Garringer H.J., Gelpi E., Newell K.L., Kovacs G.G., Vidal R., Ghetti B., Ryskeldi-Falcon B., Scheres S.H.W. and Goedert M. (2022). Cryo-EM structures of amyloid-β 42 filaments from human brains. In: «Science», 375: 167-172. Doi: doi:10.1126/science.abm7285.