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:

PROTEIN STRUCTURE PREDICTION

A language model beats alphafold2 on orphans

Nature Biotechnology volume 40, pages 1576–1577 (2022)Cite this article

Subjects

Protein structure prediction with a language model improves accuracy for orphan and designed proteins.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Fig. 1: Distance restraints from experiment or language models in protein structure calculations.

References

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Chowdhury, R. et al. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01432-w (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Pearson, W. R. Curr. Protoc. Bioinformatics Ch. 3, Unit 3.1 (2013).

  5. Perdigão, N. et al. Proc. Natl Acad. Sci. USA 112, 15898–15903 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M. & Church, G. M. Nat. Methods 16, 1315–1322 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Riesselman, A. J., Ingraham, J. B. & Marks, D. S. Nat. Methods 15, 816–822 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hie, B., Zhong, E. D., Berger, B. & Bryson, B. Science 371, 284–288 (2021).

    Article  CAS  PubMed  Google Scholar 

  9. Anishchenko, I. et al. Nature 600, 547–552 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Madani, A. et al. Preprint at bioRxiv https://doi.org/10.1101/2021.07.18.452833 (2021).

  11. AlQuraishi, M. AlphaFold @ CASP13: ‘What just happened?’ Some Thoughts on a Mysterious Universe https://moalquraishi.wordpress.com/2018/12/09/alphafold-casp13-what-just-happened/ (2018).

  12. AlQuraishi, M. AlphaFold2 @ CASP14: ‘It feels like one’s child has left home’. Some Thoughts on a Mysterious Universe https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ (2020).

Download references

Author information

Authors and Affiliations

  1. Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA

    Jennifer M. Michaud & James S. Fraser

  2. Profluent Bio, Oakland, CA, USA

    Ali Madani

Authors
  1. Jennifer M. Michaud
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ali Madani
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. James S. Fraser
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to James S. Fraser.

Ethics declarations

Competing interests

The authors declare no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Michaud, J.M., Madani, A. & Fraser, J.S. A language model beats alphafold2 on orphans. Nat Biotechnol 40, 1576–1577 (2022). https://doi.org/10.1038/s41587-022-01466-0

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41587-022-01466-0

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

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