├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── THIRD-PARTY-NOTICE ├── contact_map ├── README.md ├── data_preparation.py └── modeling.py ├── data ├── contact_map_utils.py ├── prepare_GO_data.py ├── prepare_data.py └── xpdb.py ├── figs └── lmgvp.png ├── interpretation ├── LM-GVP_Model_Interpretation.ipynb ├── Process_binding_site_data.ipynb └── README.md ├── lmgvp ├── data_loaders.py ├── datasets.py ├── deepfrier_utils.py ├── modules.py ├── transfer.py └── utils.py ├── requirements.txt ├── train.py └── zeroshot_mut ├── README.md └── ZeroShot.ipynb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/.gitignore -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/README.md -------------------------------------------------------------------------------- /THIRD-PARTY-NOTICE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/THIRD-PARTY-NOTICE -------------------------------------------------------------------------------- /contact_map/README.md: -------------------------------------------------------------------------------- 1 | # Contact map prediction analyses -------------------------------------------------------------------------------- /contact_map/data_preparation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/contact_map/data_preparation.py -------------------------------------------------------------------------------- /contact_map/modeling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/contact_map/modeling.py -------------------------------------------------------------------------------- /data/contact_map_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/data/contact_map_utils.py -------------------------------------------------------------------------------- /data/prepare_GO_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/data/prepare_GO_data.py -------------------------------------------------------------------------------- /data/prepare_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/data/prepare_data.py -------------------------------------------------------------------------------- /data/xpdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/data/xpdb.py -------------------------------------------------------------------------------- /figs/lmgvp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/figs/lmgvp.png -------------------------------------------------------------------------------- /interpretation/LM-GVP_Model_Interpretation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/interpretation/LM-GVP_Model_Interpretation.ipynb -------------------------------------------------------------------------------- /interpretation/Process_binding_site_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/interpretation/Process_binding_site_data.ipynb -------------------------------------------------------------------------------- /interpretation/README.md: -------------------------------------------------------------------------------- 1 | # Model Interpretation 2 | -------------------------------------------------------------------------------- /lmgvp/data_loaders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/lmgvp/data_loaders.py -------------------------------------------------------------------------------- /lmgvp/datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/lmgvp/datasets.py -------------------------------------------------------------------------------- /lmgvp/deepfrier_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/lmgvp/deepfrier_utils.py -------------------------------------------------------------------------------- /lmgvp/modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/lmgvp/modules.py -------------------------------------------------------------------------------- /lmgvp/transfer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/lmgvp/transfer.py -------------------------------------------------------------------------------- /lmgvp/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/lmgvp/utils.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/requirements.txt -------------------------------------------------------------------------------- /train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/train.py -------------------------------------------------------------------------------- /zeroshot_mut/README.md: -------------------------------------------------------------------------------- 1 | # Zero-shot mutational effect analyses 2 | -------------------------------------------------------------------------------- /zeroshot_mut/ZeroShot.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aws-samples/lm-gvp/HEAD/zeroshot_mut/ZeroShot.ipynb --------------------------------------------------------------------------------