├── CalcMetrics.xml ├── IteratedConvergence.xml ├── IteratedConvergence_GFP.xml ├── README.md ├── RelaxSimpleDesign_gfp.xml ├── SimpleDesign.xml ├── calc_metrics.sh ├── converge_it.sh ├── converge_it_gfp.sh ├── design.options ├── design_analysis.ipynb ├── design_analysis_known_mutations_only.ipynb ├── emi ├── ESM03.sh ├── ESM1.sh ├── ESM15.sh ├── FastDesign.sh ├── IC_ESM1.sh ├── IC_MIFST1.sh ├── IC_calc_metrics.sh ├── MIFST03.sh ├── MIFST1.sh ├── MIFST15.sh ├── RelaxDesign_calc_metrics.sh ├── RelaxSimpleMPNN1.sh ├── SimpleMPNN03.sh ├── SimpleMPNN1.sh ├── SimpleMPNN15.sh ├── avg03.sh ├── avg1.sh ├── avg15.sh ├── calc_metrics.sh ├── emi_LDA_ANT.joblib ├── emi_LDA_OVA.joblib ├── emi_binding.csv └── emi_designs.csv ├── environment.yaml ├── gb1 ├── ESM03.sh ├── ESM1.sh ├── ESM15.sh ├── FastDesign.sh ├── IC_ESM1.sh ├── IC_MIFST1.sh ├── IC_calc_metrics.sh ├── MIFST03.sh ├── MIFST1.sh ├── MIFST15.sh ├── RelaxDesign_calc_metrics.sh ├── RelaxSimpleMPNN1.sh ├── SimpleMPNN03.sh ├── SimpleMPNN1.sh ├── SimpleMPNN15.sh ├── avg03.sh ├── avg1.sh ├── avg15.sh ├── calc_metrics.sh ├── gb1_designs.csv ├── gb1_mutations_full_data.csv └── gb1_ridge.joblib ├── gfp ├── ESM03.sh ├── ESM1.sh ├── ESM15.sh ├── FastDesign.sh ├── IC_ESM1.sh ├── IC_MIFST1.sh ├── MIFST03.sh ├── MIFST1.sh ├── MIFST15.sh ├── RelaxSimpleMPNN1.sh ├── SimpleMPNN03.sh ├── SimpleMPNN1.sh ├── SimpleMPNN15.sh ├── avg03.sh ├── avg1.sh ├── avg15.sh ├── calc_metrics.sh ├── gfp_data.csv └── gfp_designs.csv ├── herceptin ├── ESM03.sh ├── ESM1.sh ├── ESM15.sh ├── FastDesign.sh ├── IC_ESM1.sh ├── IC_MIFST1.sh ├── IC_calc_metrics.sh ├── MIFST03.sh ├── MIFST1.sh ├── MIFST15.sh ├── RelaxDesign_calc_metrics.sh ├── RelaxSimpleMPNN1.sh ├── SimpleMPNN03.sh ├── SimpleMPNN1.sh ├── SimpleMPNN15.sh ├── avg03.sh ├── avg1.sh ├── avg15.sh ├── calc_metrics.sh ├── herceptin_designs.csv ├── lda_herceptin.joblib ├── mHER_H3_AgNeg.csv └── mHER_H3_AgPos.csv ├── model_training.ipynb └── simple_design.sh /CalcMetrics.xml: 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