Parameters of Evolutionary Scale Modeling (ESM) models

Path:/datasets/bio/esm/
URL:https://github.com/facebookresearch/esm
Downloaded:2025-02-13
Cite:
  • “A. Rives, J. Meier, T. Sercu, S. Goyal, Z. Lin, J. Liu, D. Guo, M. Ott, C.L. Zitnick, J. Ma, & R. Fergus, Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences, Proc. Natl. Acad. Sci. U.S.A. 118 (15) e2016239118, https://doi.org/10.1073/pnas.2016239118 (2021).” - “MSA Transformer. Roshan Rao, Jason Liu, Robert Verkuil, Joshua Meier, John F. Canny, Pieter Abbeel, Tom Sercu, Alexander Rives, bioRxiv 2021.02.12.430858; doi: https://doi.org/10.1101/2021.02.12.430858" - “Meier J, Rao R, Verkuil R, Liu J, Sercu T, Rives A. Language models enable zero-shot prediction of the effects of mutations on protein function, ioRxiv. 2021 doi: 10.1101/2021.07.09.450648.” - “Learning inverse folding from millions of predicted structures. Chloe Hsu, Robert Verkuil, Jason Liu, Zeming Lin, Brian Hie, Tom Sercu, Adam Lerer, Alexander Rives, bioRxiv 2022.04.10.487779; doi: https://doi.org/10.1101/2022.04.10.487779" - “Zeming Lin et al. ,Evolutionary-scale prediction of atomic-level protein structure with a language model.Science379,1123-1130(2023).DOI:10.1126/science.ade2574”
Variant:
    Bibtex:
    @article{Rives2021-bq, title = "Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences", author = "Rives, Alexander and Meier, Joshua and Sercu, Tom and Goyal,Siddharth and Lin, Zeming and Liu, Jason and Guo, Demi and Ott,Myle and Zitnick, C Lawrence and Ma, Jerry and Fergus, Rob",journal = "Proc. Natl. Acad. Sci. U. S. A.",publisher = "Proceedings of the National Academy of Sciences", volume = 118, number = 15, pages = "e2016239118", month = apr, year = 2021} @unpublished{Rao2021-gv, title = "{MSA} Transformer", author = "Rao, Roshan and Liu, Jason and Verkuil, Robert and Meier, Joshua and Canny, John F and Abbeel, Pieter and Sercu, Tom and Rives, Alexander", journal = "bioRxiv", month = feb, year = 2021} @unpublished{Meier2021-dy, title = "Language models enable zero-shot prediction of the effects of mutations on protein function", author = "Meier, Joshua and Rao, Roshan and Verkuil, Robert and Liu, Jason and Sercu, Tom and Rives, Alexander", journal = "bioRxiv", month = jul, year = 2021} @unpublished{Hsu2022-wk, title = "Learning inverse folding from millions of predicted structures", author = "Hsu, Chloe and Verkuil, Robert and Liu, Jason and Lin, Zeming and Hie, Brian and Sercu, Tom and Lerer, Adam and Rives, Alexander", journal = "bioRxiv", month = apr, year = 2022} @article{Lin2023-jf, title = "Evolutionary-scale prediction of atomic-level protein structure with a language model", author = "Lin, Zeming and Akin, Halil and Rao, Roshan and Hie, Brian and Zhu, Zhongkai and Lu, Wenting and Smetanin, Nikita and Verkuil, Robert and Kabeli, Ori and Shmueli, Yaniv and Dos Santos Costa, Allan and Fazel-Zarandi, Maryam and Sercu, Tom and Candido, Salvatore and Rives, Alexander", journal = "Science", volume = 379, number = 6637, pages =  "1123--1130", month = mar, year = 2023}