A topology-based approach is developed to better understand the relationship between protein structure and protein function.
References
Qiu, Y. & Wei, G.-W. Nat. Comput. Sci. https://doi.org/10.1038/s43588-022-00394-y (2023).
Hie, B. L. & Yang, K. K. Curr. Opin. Struct. Biol. 72, 145–152 (2022).
Rives, A. et al. Proc. Natl Acad. Sci. 118, e2016239118 (2021).
Rao, R. et al. Adv. Neural Inf. Process. Syst. 32, 9689–9701 (2019).
Bepler, T. & Berger, B. Learning protein sequence embeddings using information from structure. In International Conference on Learning Representations (ICLR, 2019).
Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M. & Church, G. M. Nat. Methods 16, 1315–1322 (2019).
Hopf, T. A. et al. Nat. Biotechnol. 35, 128–135 (2017).
Riesselman, A. J., Ingraham, J. B. & Marks, D. S. Nat. Methods 15, 816–822 (2018).
Luo, Y. et al. Nat. Commun. 12, 5743 (2021).
Notin, P. et al. Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval. In Proceedings of the 39th International Conference on Machine Learning (PMLR, 2022).
Jumper, J. et al. Nature 596, 583–589 (2021).
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Luo, Y. Sensing the shape of functional proteins with topology. Nat Comput Sci 3, 124–125 (2023). https://doi.org/10.1038/s43588-023-00404-7
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DOI: https://doi.org/10.1038/s43588-023-00404-7
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