Journal article Open Access

Mega-scale experimental analysis of protein folding stability in biology and design

Tsuboyama, Kotaro; Dauparas, Justas; Chen, Jonathan; Laine, Elodie; Behbahani, Yasser Mohseni; Weinstein, Jonathan J.; Mangan, Niall M.; Ovchinnikov, Sergey; Rocklin, Gabriel J.

Datasets and scripts for Nature manuscript titled "Mega-scale experimental analysis of protein folding stability in biology and design
"

Old bioRxiv link: https://doi.org/10.1101/2022.12.06.519132

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Processed_K50_dG_datasets.zip

    Tsuboyama2023_Dataset1_20230416.csv

    Tsuboyama2023_Dataset2_Dataset3_20230416.csv
    Single_DMS_list.csv
    Double_DMS_list.csv    
    Triple_DMS_list.csv
    Heat_maps_single_DMS.pdf
    Heat_maps_double_DMS.pdf

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

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

   Data_quality_filtering_script.ipynb

 

 

AlphaFold_model_PDBs.zip

Blueprints_for_EEHH.zip
    eehh_EA_GBB_AGBB.bp
    eehh_GG_GBB_AGBB.bp
    eehh_XX_XXX_XXXX.bp

Files (1.9 GB)
Name Size
AlphaFold_model_PDBs.zip
md5:c29317a75f28d008b2718316995902ef
14.0 MB Download
Blueprints_for_EEHH.zip
md5:2b0fc2dc5db92f64b545090c09cd2e51
2.4 kB Download
Data_tables_for_figs.zip
md5:c4b6a64345e30e1b9e2e40a266d14a68
24.1 MB Download
K50_dG_tables.zip
md5:1cd1e460db6aa907e17c1249b35fbb82
449.8 MB Download
Pipeline_figure_model.zip
md5:0a4bfc59f30d1cb79e77cda6c6bcca3d
938.4 kB Download
Pipeline_K50_dG.zip
md5:fda0397b725c4e45e96e926f08905c34
181.2 MB Download
Pipeline_qPCR_data.zip
md5:f2ec8d0eac9981f947ba71c2ebc6afd0
161.5 kB Download
Processed_K50_dG_datasets.zip
md5:f7e8c553efee734cf161ee6f2b0a09cf
1.0 GB Download
Raw_NGS_count_tables.zip
md5:f0a2c5882439001dbbb8d81b4e64fe24
242.9 MB Download
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