GitHub - AleksandraPanfilova/SKEMPIv2_benchmark

SKEMPI v2 PDB IDs that need to be manually cleaned (HETATMs): '5TAR', '2BTF', '1XD3'

These needed to be re-run with "proceed" having all 20 relax structures: '1Y33', '2J8U', '1FY8'

'3SE3', '3SE4', '2C5D' have more than one interface (e.g., AB_CD vs A_C)

Calculation processing

1AK4

LD483T,VD486P,HD487A,AD488M,ID491L,AD492P,MD496I variant not in the output -- M496 is kicked out of the PDB structure because of zero occupancy

Name		Name	Last commit message	Last commit date
.jupyter/desktop-workspaces		.jupyter/desktop-workspaces
SAFES_prisms		SAFES_prisms
slurms		slurms
.gitignore		.gitignore
Cart_ddG_SKEMPI_analysis.ipynb		Cart_ddG_SKEMPI_analysis.ipynb
DSSP_SKEMPI2.ipynb		DSSP_SKEMPI2.ipynb
Flex_ddG_SLURM.ipynb		Flex_ddG_SLURM.ipynb
Flex_ddG_file_struct.ipynb		Flex_ddG_file_struct.ipynb
H_subset_SKEMPI_2_xtal_Cart_ddG_IA.csv		H_subset_SKEMPI_2_xtal_Cart_ddG_IA.csv
Loading_cart_ddg_data.ipynb		Loading_cart_ddg_data.ipynb
N_mut_ddG_hist.pdf		N_mut_ddG_hist.pdf
README.md		README.md
Results.ipynb		Results.ipynb
Results_M1721.ipynb		Results_M1721.ipynb
Results_S2536.ipynb		Results_S2536.ipynb
Results_S2536_241025.ipynb		Results_S2536_241025.ipynb
Results_SAFES_241025.ipynb		Results_SAFES_241025.ipynb
Results_SkempiMAX.ipynb		Results_SkempiMAX.ipynb
Results_suppl.ipynb		Results_suppl.ipynb
S2536.csv		S2536.csv
S2536_entry_index.txt		S2536_entry_index.txt
SAFES_051025.csv		SAFES_051025.csv
SAFES_200925.csv		SAFES_200925.csv
SAFES_200925_2.csv		SAFES_200925_2.csv
SAFES_AF_metrics.csv		SAFES_AF_metrics.csv
SAFES_entry_index.txt		SAFES_entry_index.txt
SAFES_exp_051025.csv		SAFES_exp_051025.csv
SAFES_with_exp_val.csv		SAFES_with_exp_val.csv
SKEMPIv2_filtering_6167.ipynb		SKEMPIv2_filtering_6167.ipynb
SKEMPIv2_filtering_documented_skempiMAX.ipynb		SKEMPIv2_filtering_documented_skempiMAX.ipynb
Venn.ipynb		Venn.ipynb
batch_download.sh		batch_download.sh
cart_ddG_IAM_full.csv		cart_ddG_IAM_full.csv
cart_ddg_skempiMAX.csv		cart_ddg_skempiMAX.csv
cart_pipeline_full_struct.csv		cart_pipeline_full_struct.csv
cart_pipeline_full_struct_nb_inc.csv		cart_pipeline_full_struct_nb_inc.csv
cart_pipeline_full_struct_with_nb.csv		cart_pipeline_full_struct_with_nb.csv
cart_pipeline_full_struct_wtf.csv		cart_pipeline_full_struct_wtf.csv
duplicates.csv		duplicates.csv
figures_230725.tar.gz		figures_230725.tar.gz
flex_ddg_both_C380.csv		flex_ddg_both_C380.csv
flex_ddg_both_skempi2.csv		flex_ddg_both_skempi2.csv
flex_ddg_both_skempi2_std.csv		flex_ddg_both_skempi2_std.csv
flex_ddg_gam_skempi2.csv		flex_ddg_gam_skempi2.csv
flex_ddg_gam_skempi2_new.csv		flex_ddg_gam_skempi2_new.csv
flex_ddg_reg_skempi2.csv		flex_ddg_reg_skempi2.csv
flex_ddg_reg_skempi2_new.csv		flex_ddg_reg_skempi2_new.csv
pdb_list.txt		pdb_list.txt
prism_parser_SAFES.ipynb		prism_parser_SAFES.ipynb
ptm_dict.py		ptm_dict.py
s2536_test.csv		s2536_test.csv
safes_metrics_per_pdb.csv		safes_metrics_per_pdb.csv
skempi2_final.csv		skempi2_final.csv
skempi2_final_6167.csv		skempi2_final_6167.csv
skempi2_final_final.csv		skempi2_final_final.csv
skempi2_final_old.csv		skempi2_final_old.csv
skempi2_multi_measurements.csv		skempi2_multi_measurements.csv
skempi2_nb.csv		skempi2_nb.csv
skempi2_raw_entry_index.txt		skempi2_raw_entry_index.txt
skempi2_subsets_venn.pdf		skempi2_subsets_venn.pdf
skempiMAX.csv		skempiMAX.csv
skempiMAX_241025.csv		skempiMAX_241025.csv
skempiMAX_cart_ddg_IA.csv		skempiMAX_cart_ddg_IA.csv
skempiMAX_cart_ddg_IA_2025-10-26.csv		skempiMAX_cart_ddg_IA_2025-10-26.csv
skempiMAX_cart_ddg_IA_Flex_ddG_2025-10-25.csv		skempiMAX_cart_ddg_IA_Flex_ddG_2025-10-25.csv
skempiMAX_entry_index.txt		skempiMAX_entry_index.txt
skempi_3_hist.pdf		skempi_3_hist.pdf
skempi_v2.csv		skempi_v2.csv
variants_raw.csv		variants_raw.csv

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