Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • News & Views
  • Published:

Structural biology

Structural biology in the age of AI

How accurate is the prediction of protein structure by AlphaFold? Terwilliger et al. address this question with a rigorous assessment of the accuracy of AlphaFold-predicted structures by comparing them with experimentally determined X-ray crystallographic data.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Comparison between X-ray crystallography and Alphafold.

References

  1. Jumper, J. et al. Nature 596, 583–589 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Varadi, M. et al. Nucleic Acids Res. 50, D439–D444 (2022). D1.

    Article  CAS  PubMed  Google Scholar 

  3. Baek, M. et al. Science 373, 871–876 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Evans, R. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.10.04.463034 (2021).

  5. Lin, Z. et al. Science 379, 1123–1130 (2023).

    Article  CAS  PubMed  Google Scholar 

  6. Ourmazd, A., Moffat, K. & Lattman, E. E. Nat. Methods 19, 24–26 (2022).

    Article  CAS  PubMed  Google Scholar 

  7. Terwilliger, T. C. et al. Nat. Methods https://doi.org/10.1038/s41592-023-02087-4 (2023).

  8. Fontana, P. et al. Science 376, eabm9326 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Karelina, M., Noh, J. J. & Dror, R. O. eLife 12, RP89386 (2023).

  10. Wong, F. et al. Mol. Syst. Biol. 18, e11081 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Scardino, V., Di Filippo, J. I. & Cavasotto, C. N. iScience 26, 105920 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Krishna, R. et al. Preprint at bioRxiv https://doi.org/10.1101/2023.10.09.561603 (2023).

  13. Wallner, B. Proteins 91, 1734–1746 (2023).

    Article  CAS  PubMed  Google Scholar 

  14. Zheng, W., Wuyun, Q., Freddolino, P. L. & Zhang, Y. Proteins 91, 1684–1703 (2023).

    Article  CAS  PubMed  Google Scholar 

  15. Watson, J. L. et al. Nature 620, 1089–1100 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Alamdari, S. et al. Protein generation with evolutionary diffusion: sequence is all you need. bioRxiv Preprint at https://doi.org/10.1101/2023.09.11.556673 (2023).

Download references

Acknowledgements

I thank A. Fraser and A. Mukhopadhyay for insightful discussions. S.S. is the Gobind Khorana Chair for Cancer Drug Design at the University of British Columbia, supported by a Canada Excellence Research Chair award and by grants from the VGH Foundation, the Tai Hung Fai Charitable Foundation, and the Alzheimer Society of Canada.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sriram Subramaniam.

Ethics declarations

Competing interests

S.S. is the founder and CEO of Gandeeva Therapeutics, a drug discovery company based in Vancouver, Canada.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Subramaniam, S. Structural biology in the age of AI. Nat Methods 21, 18–19 (2024). https://doi.org/10.1038/s41592-023-02123-3

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41592-023-02123-3

Search

Quick links

Nature Briefing AI and Robotics

Sign up for the Nature Briefing: AI and Robotics newsletter — what matters in AI and robotics research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: AI and Robotics