Language models enable zero-shot prediction of the effects of mutations on protein function
Abstract
Modeling the effect of sequence variation on function is a fundamental problem for understanding and designing proteins. Since evolution encodes information about function into patterns in protein sequences, unsupervised models of variant effects can be learned from sequence data. The approach to date has been to fit a model to a family of related sequences. The conventional setting is limited, since a new model must be trained for each prediction task. We show that using only zero-shot inference, without any supervision from experimental data or additional training, protein language models capture the functional effects of sequence variation, performing at state-of-the-art.
Code References
huggingface/transformers
3 files
docs/source/fr/index.md
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1. **[ESM](model_doc/esm)** (from Meta AI) are transformer protein language models. **ESM-1b** was released with the paper [Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences](https://www.pnas.org/content/118/15/e2016239118) by Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus. **ESM-1v** was released with the paper [Language models enable zero-shot prediction of the effects of mutations on protein function](https://doi.org/10.1101/2021.07.09.450648) by Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu and Alexander Rives. **ESM-2 and ESMFold** were released with the paper [Language models of protein sequences at the scale of evolution enable accurate structure prediction](https://doi.org/10.1101/2022.07.20.500902) by Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives.
docs/source/ja/index.md
1
1. **[ESM](https://huggingface.co/docs/transformers/model_doc/esm)** (Meta AI γγ) γ―γγ©γ³γΉγγ©γΌγγΌγγγγ€γ³θ¨θͺγ’γγ«γ§γ. **ESM-1b** γ― Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus γγε
¬ιγγγη η©Άθ«ζ: [Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences](https://www.pnas.org/content/118/15/e2016239118). **ESM-1v** γ― Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu and Alexander Rivesγγγε
¬ιγγγη η©Άθ«ζ: [Language models enable zero-shot prediction of the effects of mutations on protein function](https://doi.org/10.1101/2021.07.09.450648). **ESM-2** γ¨γ**ESMFold** γ― Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives γγε
¬ιγγγη η©Άθ«ζ: [Language models of protein sequences at the scale of evolution enable accurate structure prediction](https://doi.org/10.1101/2022.07.20.500902)
docs/source/ko/index.md
1
1. **[ESM](model_doc/esm)** (from Meta AI) are transformer protein language models. **ESM-1b** was released with the paper [Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences](https://www.pnas.org/content/118/15/e2016239118) by Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus. **ESM-1v** was released with the paper [Language models enable zero-shot prediction of the effects of mutations on protein function](https://doi.org/10.1101/2021.07.09.450648) by Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu and Alexander Rives. **ESM-2 and ESMFold** were released with the paper [Language models of protein sequences at the scale of evolution enable accurate structure prediction](https://doi.org/10.1101/2022.07.20.500902) by Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives.
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