├── .gitignore ├── LICENSE ├── README.md ├── analysis ├── README.md ├── epistasis_analysis.ipynb └── pca_analysis.ipynb ├── directed-evo ├── DE_notebook.ipynb └── README.md ├── paper └── Supplementary Information - Evaluating eUniRep and other protein feature representations for in silico directed evolution.pdf ├── pre-evotuning ├── README.md ├── generate_evotune_inputs_2MS2.ipynb ├── generate_evotune_inputs_PETase.ipynb └── generate_evotune_inputs_TEM1.ipynb ├── seq_mutator ├── README.md └── mutator.py └── top-model ├── README.md └── top_training.ipynb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ivanjayapurna/low-n-protein-engineering/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ivanjayapurna/low-n-protein-engineering/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ivanjayapurna/low-n-protein-engineering/HEAD/README.md -------------------------------------------------------------------------------- /analysis/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ivanjayapurna/low-n-protein-engineering/HEAD/analysis/README.md -------------------------------------------------------------------------------- /analysis/epistasis_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ivanjayapurna/low-n-protein-engineering/HEAD/analysis/epistasis_analysis.ipynb -------------------------------------------------------------------------------- /analysis/pca_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ivanjayapurna/low-n-protein-engineering/HEAD/analysis/pca_analysis.ipynb -------------------------------------------------------------------------------- /directed-evo/DE_notebook.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ivanjayapurna/low-n-protein-engineering/HEAD/directed-evo/DE_notebook.ipynb -------------------------------------------------------------------------------- /directed-evo/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ivanjayapurna/low-n-protein-engineering/HEAD/directed-evo/README.md -------------------------------------------------------------------------------- /paper/Supplementary Information - 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