{
    "framework":  "PyTorch",
    "task":  "protein-language-modeling",
    "model":  "SaProt",
    "description":  "Structure-aware protein language modeling with amino-acid and Foldseek 3Di tokens for representation extraction, mutation-effect prediction, inverse folding, pretraining, downstream fine-tuning, and benchmark evaluation.",
    "subtasks":  [
                     "structure-aware-sequence-encoding",
                     "masked-language-model-inference",
                     "protein-embedding-extraction",
                     "zero-shot-mutation-effect-prediction",
                     "protein-inverse-folding",
                     "saprot-pretraining",
                     "downstream-finetuning",
                     "benchmark-evaluation",
                     "esm2-baseline-evaluation"
                 ],
    "entrypoints":  {
                        "train":  "scripts/training.py",
                        "pretrain_config":  "conf/pretrain/saprot.yaml",
                        "thermos_finetune_config":  "conf/Thermostability/saprot.yaml",
                        "scnet_thermos_finetune_config":  "conf/scnet/Thermostability_saprot_1gpu.yaml",
                        "mutation_zeroshot":  "scripts/mutation_zeroshot.py",
                        "proteingym_config":  "conf/ProteinGym/saprot.yaml",
                        "clinvar_config":  "conf/ClinVar/saprot.yaml",
                        "scnet_clinvar_config":  "conf/scnet/ClinVar_saprot.yaml",
                        "clinvar_auc":  "scripts/compute_clinvar_auc.py",
                        "environment_setup":  "scripts/environment.sh"
                    },
    "packages":  [
                     "model",
                     "scripts.dataset",
                     "scripts.utils"
                 ],
    "configs":  {
                    "root":  "conf",
                    "saprot_tasks":  [
                                         "conf/Thermostability/saprot.yaml",
                                         "conf/EC/saprot.yaml",
                                         "conf/GO/MF/saprot.yaml",
                                         "conf/GO/BP/saprot.yaml",
                                         "conf/GO/CC/saprot.yaml",
                                         "conf/MetalIonBinding/saprot.yaml",
                                         "conf/HumanPPI/saprot.yaml",
                                         "conf/Contact/saprot.yaml",
                                         "conf/DeepLoc/cls2/saprot.yaml",
                                         "conf/DeepLoc/cls10/saprot.yaml",
                                         "conf/ProteinGym/saprot.yaml",
                                         "conf/ClinVar/saprot.yaml"
                                     ],
                    "esm2_baselines":  [
                                           "conf/Thermostability/esm2.yaml",
                                           "conf/EC/esm2.yaml",
                                           "conf/GO/MF/esm2.yaml",
                                           "conf/GO/BP/esm2.yaml",
                                           "conf/GO/CC/esm2.yaml",
                                           "conf/MetalIonBinding/esm2.yaml",
                                           "conf/HumanPPI/esm2.yaml",
                                           "conf/Contact/esm2.yaml",
                                           "conf/DeepLoc/cls2/esm2.yaml",
                                           "conf/DeepLoc/cls10/esm2.yaml",
                                           "conf/ProteinGym/esm2.yaml",
                                           "conf/ClinVar/esm2.yaml"
                                       ],
                    "scnet":  [
                                  "conf/scnet/Thermostability_saprot_1gpu.yaml",
                                  "conf/scnet/ClinVar_saprot.yaml"
                              ]
                },
    "example_data":  [
                         "scripts/example/8ac8.cif"
                     ],
    "data_roots":  {
                       "downstream_lmdb":  "scripts/LMDB",
                       "pretrain_lmdb":  "scripts/LMDB/AF2_Uniref50/foldseek",
                       "proteingym":  "scripts/LMDB/ProteinGym/substitutions",
                       "clinvar":  "scripts/LMDB/ClinVar",
                       "thermos":  "scripts/LMDB/Thermostability/foldseek"
                   },
    "model_cache":  "weight/PLMs",
    "default_model":  "weight/PLMs/SaProt_650M_AF2",
    "optional_models":  {
                            "esm2_650m":  "weight/PLMs/esm2_t33_650M_UR50D",
                            "saprot_inverse_folding":  "weight/PLMs/SaProt_650M_AF2_inverse_folding"
                        },
    "external_tools":  {
                           "foldseek":  "scripts/bin/foldseek"
                       },
    "outputs":  {
                    "finetuned_checkpoints":  "weight/{task}/*.pt",
                    "proteingym_scores":  "output/ProteinGym/SaProt_650M_AF2.tsv",
                    "clinvar_predictions":  "output/ClinVar/SaProt_650M_AF2",
                    "scnet_clinvar_predictions":  "output/ClinVar/SaProt_650M_AF2_scnet"
                },
    "quick_commands":  {
                           "setup":  "bash scripts/environment.sh",
                           "train_thermostability":  "python scripts/training.py -c conf/Thermostability/saprot.yaml",
                           "train_thermostability_scnet_1gpu":  "python scripts/training.py -c conf/scnet/Thermostability_saprot_1gpu.yaml",
                           "zeroshot_proteingym":  "python scripts/mutation_zeroshot.py -c conf/ProteinGym/saprot.yaml",
                           "zeroshot_clinvar":  "python scripts/mutation_zeroshot.py -c conf/ClinVar/saprot.yaml",
                           "compute_clinvar_auc":  "python scripts/compute_clinvar_auc.py -c conf/ClinVar/saprot.yaml"
                       }
}