├── LICENSE ├── README.md ├── configs ├── 1n8z.yaml └── 5ngv.yaml ├── data ├── Afasevikumab-IL17A.csv ├── Bimagrumab-ACVR2B.csv ├── Blinded │ └── Ravagalimab-CD40.csv ├── Eculizumab-C5.csv ├── Osocimab-FXI.csv ├── Sensorgrams │ ├── Afasevikumab-IL17A.pdf │ ├── Bimagrumab-ACVR2B.pdf │ ├── Eculizumab-C5.pdf │ ├── Osocimab-FXI.pdf │ ├── Ravagalimab-CD40.pdf │ ├── Spesolimab-IL36R.pdf │ ├── Tezepelumab-TSLP.pdf │ └── Utomilumab-TNFRSF9.pdf ├── Spesolimab-IL36R.csv ├── Tezepelumab-TSLP.csv └── Utomilumab-TNFRSF9.csv ├── download_ckpts.sh ├── environment-amd.yml ├── environment.yml ├── examples ├── 1n8z.pdb └── 5ngv.pdb ├── install_amd_env.sh ├── predict.py ├── setup.py └── src └── igdesign ├── data ├── datasets │ ├── pdb_antibody.py │ └── structural.py ├── pdb_parser.py └── structure_analysis.py ├── embedding.py ├── features ├── feature.py ├── feature_constants.py ├── feature_factory.py ├── feature_utils.py └── generator.py ├── inference_utils.py ├── model.py ├── model_wrapper.py ├── models ├── lmdesign_model.py └── reformer.py ├── protein_mpnn.py ├── structure_utils.py ├── tokenization.py └── utils.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/README.md -------------------------------------------------------------------------------- /configs/1n8z.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/configs/1n8z.yaml -------------------------------------------------------------------------------- /configs/5ngv.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/configs/5ngv.yaml -------------------------------------------------------------------------------- /data/Afasevikumab-IL17A.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Afasevikumab-IL17A.csv -------------------------------------------------------------------------------- /data/Bimagrumab-ACVR2B.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Bimagrumab-ACVR2B.csv -------------------------------------------------------------------------------- /data/Blinded/Ravagalimab-CD40.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Blinded/Ravagalimab-CD40.csv -------------------------------------------------------------------------------- /data/Eculizumab-C5.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Eculizumab-C5.csv -------------------------------------------------------------------------------- /data/Osocimab-FXI.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Osocimab-FXI.csv -------------------------------------------------------------------------------- /data/Sensorgrams/Afasevikumab-IL17A.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Sensorgrams/Afasevikumab-IL17A.pdf -------------------------------------------------------------------------------- /data/Sensorgrams/Bimagrumab-ACVR2B.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Sensorgrams/Bimagrumab-ACVR2B.pdf -------------------------------------------------------------------------------- /data/Sensorgrams/Eculizumab-C5.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Sensorgrams/Eculizumab-C5.pdf -------------------------------------------------------------------------------- /data/Sensorgrams/Osocimab-FXI.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Sensorgrams/Osocimab-FXI.pdf -------------------------------------------------------------------------------- /data/Sensorgrams/Ravagalimab-CD40.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Sensorgrams/Ravagalimab-CD40.pdf -------------------------------------------------------------------------------- /data/Sensorgrams/Spesolimab-IL36R.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Sensorgrams/Spesolimab-IL36R.pdf -------------------------------------------------------------------------------- /data/Sensorgrams/Tezepelumab-TSLP.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Sensorgrams/Tezepelumab-TSLP.pdf -------------------------------------------------------------------------------- /data/Sensorgrams/Utomilumab-TNFRSF9.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Sensorgrams/Utomilumab-TNFRSF9.pdf -------------------------------------------------------------------------------- /data/Spesolimab-IL36R.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Spesolimab-IL36R.csv -------------------------------------------------------------------------------- /data/Tezepelumab-TSLP.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Tezepelumab-TSLP.csv -------------------------------------------------------------------------------- /data/Utomilumab-TNFRSF9.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/data/Utomilumab-TNFRSF9.csv -------------------------------------------------------------------------------- /download_ckpts.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/download_ckpts.sh -------------------------------------------------------------------------------- /environment-amd.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/environment-amd.yml -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/environment.yml -------------------------------------------------------------------------------- /examples/1n8z.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/examples/1n8z.pdb -------------------------------------------------------------------------------- /examples/5ngv.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/examples/5ngv.pdb -------------------------------------------------------------------------------- /install_amd_env.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/install_amd_env.sh -------------------------------------------------------------------------------- /predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/predict.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/setup.py -------------------------------------------------------------------------------- /src/igdesign/data/datasets/pdb_antibody.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/data/datasets/pdb_antibody.py -------------------------------------------------------------------------------- /src/igdesign/data/datasets/structural.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/data/datasets/structural.py -------------------------------------------------------------------------------- /src/igdesign/data/pdb_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/data/pdb_parser.py -------------------------------------------------------------------------------- /src/igdesign/data/structure_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/data/structure_analysis.py -------------------------------------------------------------------------------- /src/igdesign/embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/embedding.py -------------------------------------------------------------------------------- /src/igdesign/features/feature.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/features/feature.py -------------------------------------------------------------------------------- /src/igdesign/features/feature_constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/features/feature_constants.py -------------------------------------------------------------------------------- /src/igdesign/features/feature_factory.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/features/feature_factory.py -------------------------------------------------------------------------------- /src/igdesign/features/feature_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/features/feature_utils.py -------------------------------------------------------------------------------- /src/igdesign/features/generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/features/generator.py -------------------------------------------------------------------------------- /src/igdesign/inference_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/inference_utils.py -------------------------------------------------------------------------------- /src/igdesign/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/model.py -------------------------------------------------------------------------------- /src/igdesign/model_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/model_wrapper.py -------------------------------------------------------------------------------- /src/igdesign/models/lmdesign_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/models/lmdesign_model.py -------------------------------------------------------------------------------- /src/igdesign/models/reformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/models/reformer.py -------------------------------------------------------------------------------- /src/igdesign/protein_mpnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/protein_mpnn.py -------------------------------------------------------------------------------- /src/igdesign/structure_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/structure_utils.py -------------------------------------------------------------------------------- /src/igdesign/tokenization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/tokenization.py -------------------------------------------------------------------------------- /src/igdesign/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AbSciBio/igdesign/HEAD/src/igdesign/utils.py --------------------------------------------------------------------------------