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config.json
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config.json
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{
"PG_data_location": "~/.cache/proteingym",
"model_list_zero_shot_substitutions_DMS":{
"Site_Independent":{"input_score_name":"prediction_independent", "location":"EVmutation", "directionality": 1, "key": "mutant", "model_type":"Alignment-based model"},
"EVmutation":{"input_score_name":"prediction_epistatic", "location":"EVmutation", "directionality": 1, "key": "mutant", "model_type":"Alignment-based model"},
"DeepSequence_single":{"input_score_name":"evol_indices_seed_1000", "location":"DeepSequence", "directionality": -1, "key": "mutant","model_type":"Alignment-based model"},
"DeepSequence_ensemble":{"input_score_name":"evol_indices_ensemble", "location":"DeepSequence", "directionality": -1, "key": "mutant","model_type":"Alignment-based model"},
"EVE_single":{"input_score_name":"evol_indices_seed_1000", "location":"EVE", "directionality": -1, "key": "mutant","model_type":"Alignment-based model"},
"EVE_ensemble":{"input_score_name":"evol_indices_ensemble", "location":"EVE", "directionality": -1, "key": "mutant","model_type":"Alignment-based model"},
"Unirep":{"input_score_name":"Unirep_score", "location":"UniRep", "directionality": -1, "key": "mutated_sequence","model_type":"Protein language model"},
"Unirep_evotune":{"input_score_name":"Unirep_score", "location":"UniRep_evotuned", "directionality": -1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"MSA_Transformer_single":{"input_score_name":"esm_msa1b_t12_100M_UR50S_seed1", "location":"MSA_Transformer", "directionality": 1, "key": "mutant","model_type":"Hybrid - Alignment & PLM"},
"MSA_Transformer_ensemble":{"input_score_name":"esm_msa1b_t12_100M_UR50S_ensemble", "location":"MSA_Transformer", "directionality": 1, "key": "mutant","model_type":"Hybrid - Alignment & PLM"},
"ESM1b":{"input_score_name":"esm1b_t33_650M_UR50S", "location":"ESM1b", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ESM1v_single":{"input_score_name":"esm1v_t33_650M_UR90S_1", "location":"ESM1v", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ESM1v_ensemble":{"input_score_name":"Ensemble_ESM1v", "location":"ESM1v", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ESM2_8M":{"input_score_name":"esm2_t6_8M_UR50D", "location":"ESM2/8M", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ESM2_35M":{"input_score_name":"esm2_t12_35M_UR50D", "location":"ESM2/35M", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ESM2_150M":{"input_score_name":"esm2_t30_150M_UR50D", "location":"ESM2/150M", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ESM2_650M":{"input_score_name":"esm2_t33_650M_UR50D", "location":"ESM2/650M", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ESM2_3B":{"input_score_name":"esm2_t36_3B_UR50D", "location":"ESM2/3B", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ESM2_15B":{"input_score_name":"esm2_t48_15B_UR50D", "location":"ESM2/15B", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Wavenet":{"input_score_name":"Wavenet_prediction", "location":"Wavenet", "directionality": -1, "key": "mutant","model_type":"Alignment-based model"},
"RITA_s":{"input_score_name":"RITA_score", "location":"RITA/small", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"RITA_m":{"input_score_name":"RITA_score", "location":"RITA/medium", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"RITA_l":{"input_score_name":"RITA_score", "location":"RITA/large", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"RITA_xl":{"input_score_name":"RITA_score", "location":"RITA/xlarge", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_small":{"input_score_name":"Progen2_score", "location":"Progen2/small", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_medium":{"input_score_name":"Progen2_score", "location":"Progen2/medium", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_base":{"input_score_name":"Progen2_score", "location":"Progen2/base", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_large":{"input_score_name":"Progen2_score", "location":"Progen2/large", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_xlarge":{"input_score_name":"Progen2_score", "location":"Progen2/xlarge", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"GEMME":{"input_score_name":"GEMME_score", "location":"GEMME", "directionality": 1, "key": "mutant","model_type":"Alignment-based model"},
"VESPA":{"input_score_name":"VESPA", "location":"VESPA", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"VESPAl":{"input_score_name":"VESPAl", "location":"VESPA", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ProtGPT2":{"input_score_name":"ProtGPT2_score", "location":"ProtGPT2", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_S_no_retrieval":{"input_score_name":"avg_score", "location":"Tranception_no_retrieval/Tranception_S", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_M_no_retrieval":{"input_score_name":"avg_score", "location":"Tranception_no_retrieval/Tranception_M", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_L_no_retrieval":{"input_score_name":"avg_score", "location":"Tranception_no_retrieval/Tranception_L", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_S":{"input_score_name":"avg_score", "location":"Tranception/Tranception_S", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"Tranception_M":{"input_score_name":"avg_score", "location":"Tranception/Tranception_M", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"Tranception_L":{"input_score_name":"avg_score", "location":"Tranception/Tranception_L", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"TranceptEVE_S":{"input_score_name":"avg_score", "location":"TranceptEVE/TranceptEVE_S", "directionality": 1, "key": "mutant","model_type":"Hybrid - Alignment & PLM"},
"TranceptEVE_M":{"input_score_name":"avg_score", "location":"TranceptEVE/TranceptEVE_M", "directionality": 1, "key": "mutant","model_type":"Hybrid - Alignment & PLM"},
"TranceptEVE_L":{"input_score_name":"avg_score", "location":"TranceptEVE/TranceptEVE_L", "directionality": 1, "key": "mutant","model_type":"Hybrid - Alignment & PLM"},
"CARP_38M": {"input_score_name":"carp_38M_score","location":"CARP/carp_38M","directionality":1,"key":"mutant","model_type":"Protein language model"},
"CARP_600K": {"input_score_name":"carp_600k_score","location":"CARP/carp_600k","directionality":1,"key":"mutant","model_type":"Protein language model"},
"CARP_640M" : {"input_score_name":"carp_640M_score","location":"CARP/carp_640M","directionality":1,"key":"mutant","model_type":"Protein language model"},
"CARP_76M": {"input_score_name":"carp_76M_score","location":"CARP/carp_76M","directionality":1,"key":"mutant","model_type":"Protein language model"},
"MIF": {"input_score_name": "mif_score","location":"MIF/mif","directionality":1,"key":"mutant","model_type":"Inverse folding model"},
"MIFST":{ "input_score_name": "mifst_score","location":"MIF/mifst","directionality":1,"key":"mutant","model_type":"Hybrid - Structure & PLM"},
"ESM-IF1": {"input_score_name": "esmif1_ll","location":"ESM-IF1","directionality":1,"key":"mutant","model_type":"Inverse folding model"},
"ProteinMPNN": {"input_score_name": "pmpnn_ll","location":"ProteinMPNN","directionality":1,"key":"mutant","model_type":"Inverse folding model"},
"ProtSSN_k10_h512":{"input_score_name":"ProtSSN_k10_h512", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_k10_h768":{"input_score_name":"ProtSSN_k10_h768", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_k10_h1280":{"input_score_name":"ProtSSN_k10_h1280", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_k20_h512":{"input_score_name":"ProtSSN_k20_h512", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_k20_h768":{"input_score_name":"ProtSSN_k20_h768", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_k20_h1280":{"input_score_name":"ProtSSN_k20_h1280", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_k30_h512":{"input_score_name":"ProtSSN_k30_h512", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_k30_h768":{"input_score_name":"ProtSSN_k30_h768", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_k30_h1280":{"input_score_name":"ProtSSN_k30_h1280", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"},
"ProtSSN_ensemble":{"input_score_name":"ProtSSN_ensemble", "location":"ProtSSN", "directionality": 1, "key": "mutant","model_type":"Hybrid - Structure & PLM"}
},
"model_list_zero_shot_indels_DMS":{
"Unirep":{"input_score_name":"Unirep_score", "location":"UniRep", "directionality": -1, "key": "mutated_sequence","model_type":"Protein language model"},
"Wavenet":{"input_score_name":"Wavenet_prediction", "location":"Wavenet", "directionality": -1, "key": "mutated_sequence","model_type":"Alignment-based model"},
"RITA_s":{"input_score_name":"RITA_score", "location":"RITA/small", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"RITA_m":{"input_score_name":"RITA_score", "location":"RITA/medium", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"RITA_l":{"input_score_name":"RITA_score", "location":"RITA/large", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"RITA_xl":{"input_score_name":"RITA_score", "location":"RITA/xlarge", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_small":{"input_score_name":"Progen2_score", "location":"Progen2/small", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_medium":{"input_score_name":"Progen2_score", "location":"Progen2/medium", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_base":{"input_score_name":"Progen2_score", "location":"Progen2/base", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_large":{"input_score_name":"Progen2_score", "location":"Progen2/large", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"Progen2_xlarge":{"input_score_name":"Progen2_score", "location":"Progen2/xlarge", "directionality": 1, "key": "mutant","model_type":"Protein language model"},
"ProtGPT2":{"input_score_name":"ProtGPT2_score", "location":"ProtGPT2", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_S_no_retrieval":{"input_score_name":"avg_score", "location":"Tranception_no_retrieval/Tranception_S", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_M_no_retrieval":{"input_score_name":"avg_score", "location":"Tranception_no_retrieval/Tranception_M", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_L_no_retrieval":{"input_score_name":"avg_score", "location":"Tranception_no_retrieval/Tranception_L", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_S":{"input_score_name":"avg_score", "location":"Tranception/Tranception_S", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"Tranception_M":{"input_score_name":"avg_score", "location":"Tranception/Tranception_M", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"Tranception_L":{"input_score_name":"avg_score", "location":"Tranception/Tranception_L", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"TranceptEVE_S":{"input_score_name":"avg_score", "location":"TranceptEVE/TranceptEVE_S", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"TranceptEVE_M":{"input_score_name":"avg_score", "location":"TranceptEVE/TranceptEVE_M", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"TranceptEVE_L":{"input_score_name":"avg_score", "location":"TranceptEVE/TranceptEVE_L", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"HMM":{"input_score_name":"logprob", "location":"HMM", "directionality": 1, "key": "mutant","model_type":"Alignment-based model"},
"Provean":{"input_score_name":"Provean_score","location":"Provean","directionality":1,"key":"mutant","model_type":"Alignment-based model"}
},
"model_list_zero_shot_indels_clinical":{
"HMM":{"input_score_name":"logprob", "location":"HMM", "directionality": 1, "key": "mutated_sequence","model_type":"Alignment-based model"},
"Progen2_small":{"input_score_name":"Progen2_score", "location":"Progen2/small", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Progen2_medium":{"input_score_name":"Progen2_score", "location":"Progen2/medium", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Progen2_base":{"input_score_name":"Progen2_score", "location":"Progen2/base", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Progen2_large":{"input_score_name":"Progen2_score", "location":"Progen2/large", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Progen2_xlarge":{"input_score_name":"Progen2_score", "location":"Progen2/xlarge", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"ProtGPT2":{"input_score_name":"ProtGPT2_score", "location":"ProtGPT2", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Provean":{"input_score_name":"provean_score","location":"Provean","directionality":1,"key":"mutated_sequence","model_type":"Alignment-based model"},
"RITA_s":{"input_score_name":"RITA_score", "location":"RITA/small", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"RITA_m":{"input_score_name":"RITA_score", "location":"RITA/medium", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"RITA_l":{"input_score_name":"RITA_score", "location":"RITA/large", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"RITA_xl":{"input_score_name":"RITA_score", "location":"RITA/xlarge", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_M_no_retrieval":{"input_score_name":"avg_score", "location":"Tranception_no_retrieval/Tranception_M", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_L_no_retrieval":{"input_score_name":"avg_score", "location":"Tranception_no_retrieval/Tranception_L", "directionality": 1, "key": "mutated_sequence","model_type":"Protein language model"},
"Tranception_M":{"input_score_name":"avg_score", "location":"Tranception/Tranception_M", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"Tranception_L":{"input_score_name":"avg_score", "location":"Tranception/Tranception_L", "directionality": 1, "key": "mutated_sequence","model_type":"Hybrid - Alignment & PLM"},
"Unirep":{"input_score_name":"Unirep_score", "location":"Unirep", "directionality": -1, "key": "mutated_sequence","model_type":"Protein language model"}
},
"model_list_zero_shot_substitutions_clinical":{
"ClinPred":{"input_score_name":"ClinPred_score", "location":"ClinPred", "directionality": 1, "key": "mutant","model_type":"Clinical Predictor"},
"DANN":{"input_score_name":"DANN_score", "location":"DANN", "directionality": 1, "key": "mutant","model_type":"Clinical Predictor"},
"MutationTaster":{"input_score_name":"MutationTaster_converted_rankscore","location":"MutationTaster","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"CADD":{"input_score_name":"CADD_phred","location":"CADD","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"FATHMM":{"input_score_name":"FATHMM_score","location":"FATHMM","directionality":-1,"key":"mutant","model_type":"Clinical Predictor"},
"LRT":{"input_score_name":"LRT_score","location":"LRT","directionality":-1,"key":"mutant","model_type":"Clinical Predictor"},
"LIST-S2":{"input_score_name":"LIST-S2_score","location":"LIST-S2","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"PrimateAI":{"input_score_name":"PrimateAI_score","location":"PrimateAI","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"MutPred":{"input_score_name":"MutPred_score","location":"MutPred","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"MutationAssessor":{"input_score_name":"MutationAssessor_score","location":"MutationAssessor","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"SIFT4G":{"input_score_name":"SIFT4G_score","location":"SIFT4G","directionality":-1,"key":"mutant","model_type":"Clinical Predictor"},
"SIFT":{"input_score_name":"SIFT_score","location":"SIFT","directionality":-1,"key":"mutant","model_type":"Clinical Predictor"},
"PolyPhen2 (HDIV)":{ "input_score_name":"Polyphen2_HDIV_score","location":"Polyphen2_HDIV","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"MPC":{"input_score_name":"MPC_score","location":"MPC","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"Provean":{"input_score_name":"PROVEAN_score","location":"PROVEAN","directionality":-1,"key":"mutant","model_type":"Clinical Predictor"},
"DEOGEN2":{"input_score_name":"DEOGEN2_score","location":"DEOGEN2","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"PolyPhen2 (HVAR)":{"input_score_name":"Polyphen2_HVAR_score","location":"Polyphen2_HVAR","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"gMVP":{"input_score_name":"gMVP_score","location":"gMVP","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"VARITY (R)":{ "input_score_name":"VARITY_R_LOO_score","location":"VARITY_R_LOO","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"VARITY (ER)":{ "input_score_name":"VARITY_ER_LOO_score","location":"VARITY_ER_LOO","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"BayesDel (addAF)":{ "input_score_name":"BayesDel_addAF_score","location":"BayesDel_addAF","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"BayesDel (noAF)":{ "input_score_name":"BayesDel_noAF_score","location":"BayesDel_noAF","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"REVEL":{"input_score_name":"REVEL_score","location":"REVEL","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"VEST4":{"input_score_name":"VEST4_score","location":"VEST4","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"MetaRNN":{"input_score_name":"MetaRNN_score","location":"MetaRNN","directionality":1,"key":"mutant","model_type":"Clinical Predictor"},
"TranceptEVE_L":{"input_score_name":"avg_score", "location":"TranceptEVE/TranceptEVE_L", "directionality": 1, "key": "mutant","model_type":"Hybrid - Alignment & PLM"},
"GEMME":{"input_score_name":"GEMME_score", "location":"GEMME", "directionality": 1, "key": "mutant","model_type":"Alignment-based model"},
"EVE":{"input_score_name":"EVE_evol_index", "location":"EVE", "directionality": -1, "key": "mutant","model_type":"Alignment-based model"},
"ESM1b":{"input_score_name":"esm1b_t33_650M_UR50S", "location":"ESM1b", "directionality": 1, "key": "mutant","model_type":"Protein language model"}
}
}