godotgildor/cdna-display-proteolysis-pipeline

cdna-display-proteolysis-pipeline

Description

• This repo includes only scripts related to a manuscript titled "Mega-scale experimental analysis of protein folding stability in biology and protein design"
• URL: https://www.biorxiv.org/content/10.1101/2022.12.06.519132v1
• You can find the following all tables required for the pipelines above here
• URL: https://doi.org/10.5281/zenodo.7401275

Scripts on github

Pipeline_K50_dG (a main pipeline to generate K50/dG [folding stability] from NGS data)

STEP1_module.ipynb
STEP1_run.ipynb
STEP2_run.ipynb
STEP3_run.ipynb
STEP4_module.ipynb
STEP4_run.ipynb
STEP5_module.ipynb
STEP5_run.ipynb
Raw_NGS_counts_overlapped_seqs_STEP1_lib1_lib2.csv
Raw_NGS_counts_overlapped_seqs_STEP1_lib2_lib3.csv
Raw_NGS_counts_overlapped_seqs_STEP1_lib1_lib4.csv
Raw_NGS_counts_overlapped_seqs_STEP1_lib2_lib4.csv
Raw_NGS_counts_overlapped_seqs_STEP1_lib3_lib4.csv
STEP1_out_protease_concentration_trypsin
STEP1_out_protease_concentration_chymotrypsin

Pipeline_figure_model

Burial_side_chain_contact_Fig3_Fig6.ipynb
Additive_model_Fig4.ipynb
Classification_model_Fig5.ipynb

Pipeline_qPCR_data: a pipeline to analyze qPCR data (related to Fig. S1)

Raw_qPCR_data_FigS1.csv
Process_qPCR_data.ipynb

Files on Zenodo

Raw_NGS_count_tables.zip

NGS_count_lib1.csv
NGS_count_lib2.csv
NGS_count_lib3.csv
NGS_count_lib4.csv

K50_dG_tables.zip

K50_dG_lib1.csv
K50_dG_lib2.csv
K50_dG_lib3.csv
K50_dG_lib4.csv

Processed_K50_dG_datasets.zip

K50_dG_Dataset1_Dataset2.csv
K50_Dataset3.csv
Single_DMS_list.csv
Double_DMS_list.csv	
Triple_DMS_list.csv
Heat_maps_single_DMS.pdf
Heat_maps_double_DMS.pdf

Data_tables_for_figs.zip

dG_extdG_data_Fig1.csv
dG_site_feature_Fig3.csv
dG_for_double_mutants_Fig4.csv
dG_non_redundant_natural_Fig5.csv
dG_GEMME_non_redundant_natural_Fig6.csv

Pipeline_qPCR_data.zip

Raw_qPCR_data_FigS1.csv
Process_qPCR_data.ipynb

Pipeline_K50_dG.zip

STEP1_module.ipynb
STEP1_run.ipynb
STEP2_run.ipynb
STEP3_run.ipynb
STEP4_module.ipynb
STEP4_run.ipynb
STEP5_module.ipynb
STEP5_run.ipynb
Raw_NGS_counts_overlapped_seqs_STEP1_lib1_lib2.csv
Raw_NGS_counts_overlapped_seqs_STEP1_lib2_lib3.csv
Raw_NGS_counts_overlapped_seqs_STEP1_lib1_lib4.csv
Raw_NGS_counts_overlapped_seqs_STEP1_lib2_lib4.csv
Raw_NGS_counts_overlapped_seqs_STEP1_lib3_lib4.csv
K50_scrambles_for_STEP3.csv
STEP1_out_protease_concentration_trypsin
STEP1_out_protease_concentration_chymotrypsin
STEP3_unfolded_model_params

Pipeline_figure_model.zip

Burial_side_chain_contact_Fig3_Fig6.ipynb
Additive_model_Fig4.ipynb
Classification_model_Fig5.ipynb

AlphaFold_model_PDBs.zip

Blueprints_for_EEHH.zip

eehh_EA_GBB_AGBB.bp
eehh_GG_GBB_AGBB.bp
eehh_XX_XXX_XXXX.bp