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--- |
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base_model: westlake-repl/SaProt_35M_AF2 |
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library_name: peft |
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--- |
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# Base model: [westlake-repl/SaProt_35M_AF2](https://huggingface.co/westlake-repl/SaProt_35M_AF2) |
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# Model Card for Model ID |
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<!-- Provide a quick summary of what the model is/does. --> |
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This model is used to predict fitness of mutant β-subunit of tryptophan synthase (TrpB). |
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TrpB synthesizes L-tryptophan (Trp) from indole and L-serine (Ser). |
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TrpB variant Tm9D8*, derived from the hyperthermophile Thermotoga maritima, was selected as the parent enzyme. |
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Tm9D8* differs from wildtype TmTrpB by ten amino acid substitutions (P19G, E30G, I69V, K96L, P140L, N167D, I184F, L213P, G228S, and T292S). |
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### Task type |
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protein level regression |
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### Dataset description |
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The dataset is from [A combinatorially complete epistatic fitness landscape in an enzyme active site](https://www.biorxiv.org/content/10.1101/2024.06.23.600144v1). |
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The dataset can also be found at [SaProtHub dataset](https://huggingface.co/datasets/SaProtHub/TrpB_fitness_landsacpe_dataset). |
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Label means mutation fitness, here represents growth rate of E. coli strain. The maximum fitness is 1, the closer to 1, the better fitness. |
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### Model input type |
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Amino acid sequence |
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### Performance |
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test_pearson: 0.93 |
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test_spearman: 0.38 |
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### LoRA config |
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lora_dropout: 0.0 |
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lora_alpha: 16 |
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target_modules: ["query", "key", "value", "intermediate.dense", "output.dense"] |
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modules_to_save: ["classifier"] |
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### Training config |
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class: AdamW |
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betas: (0.9, 0.98) |
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weight_decay: 0.01 |
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learning rate: 5e-4 |
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epoch: 100 |
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batch size: 100 |
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precision: 16-mixed |
