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README.md
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# **ZymCTRL**
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ZymCTRL (Enzyme Control) ([ see preprint ](https://www.biorxiv.org/content/10.1101/2024.05.03.592223v1))
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is a conditional language model for the generation of artificial functional enzymes. It was trained on
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Given a user-defined Enzymatic Commission (EC) number, the model generates protein sequences that fulfill that catalytic reaction.
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The generated sequences are ordered, globular, and distant to natural ones, while their intended catalytic properties match those defined by users.
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If you don't know the EC number of your protein of interest, have a look
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See below for information about the model, how to generate sequences, and how to save and rank them by perplexity.
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ZymCTRL is based on the [CTRL Transformer](https://arxiv.org/abs/1909.05858) architecture (which in turn is very similar to ChatGPT) and contains 36 layers
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with a model dimensionality of 1280, totaling 738 million parameters.
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ZymCTRL is a decoder-only transformer model pre-trained on the
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(version July 2022). The pre-training was done on the raw sequences without FASTA headers,
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with the EC classes prepended to each sequence. The databases will be uploaded soon.
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# **ZymCTRL**
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ZymCTRL (Enzyme Control) ([ see preprint ](https://www.biorxiv.org/content/10.1101/2024.05.03.592223v1))
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is a conditional language model for the generation of artificial functional enzymes. It was trained on Uniprot database of sequences containing EC annotations, comprising over 37 M sequences.
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Given a user-defined Enzymatic Commission (EC) number, the model generates protein sequences that fulfill that catalytic reaction.
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The generated sequences are ordered, globular, and distant to natural ones, while their intended catalytic properties match those defined by users.
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If you don't know the EC number of your protein of interest, have a look for example here: https://www.brenda-enzymes.org/ecexplorer.php?browser=1
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See below for information about the model, how to generate sequences, and how to save and rank them by perplexity.
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ZymCTRL is based on the [CTRL Transformer](https://arxiv.org/abs/1909.05858) architecture (which in turn is very similar to ChatGPT) and contains 36 layers
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with a model dimensionality of 1280, totaling 738 million parameters.
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ZymCTRL is a decoder-only transformer model pre-trained on the Uniprot subset of enzyme sequences, totalling 37M sequences.
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(version July 2022). The pre-training was done on the raw sequences without FASTA headers,
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with the EC classes prepended to each sequence. The databases will be uploaded soon.
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