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2epitope_escape.csv
2epitope_escape.csv
 
 
2epitope_model_curve_specs.csv
2epitope_model_curve_specs.csv
 
 
6M0J.pdb
6M0J.pdb
 
 
BA.1_site_numbering_map.csv
BA.1_site_numbering_map.csv
 
 
Env_site_numbering_map.csv
Env_site_numbering_map.csv
 
 
Env_trimer.pdb
Env_trimer.pdb
 
 
Lib-2_2022-06-22_thaw-1_LyCoV-1404_1_prob_escape.csv
Lib-2_2022-06-22_thaw-1_LyCoV-1404_1_prob_escape.csv
 
 
Omicron_BA.1_muteffects_observed.csv
Omicron_BA.1_muteffects_observed.csv
 
 
RBD_activity_wt_df.csv
RBD_activity_wt_df.csv
 
 
RBD_average.ipynb
RBD_average.ipynb
 
 
RBD_bootstrap.ipynb
RBD_bootstrap.ipynb
 
 
RBD_mean_class_1.pdb
RBD_mean_class_1.pdb
 
 
RBD_mean_class_1.png
RBD_mean_class_1.png
 
 
RBD_mean_class_2.pdb
RBD_mean_class_2.pdb
 
 
RBD_mean_class_2.png
RBD_mean_class_2.png
 
 
RBD_mean_class_3.pdb
RBD_mean_class_3.pdb
 
 
RBD_mean_class_3.png
RBD_mean_class_3.png
 
 
RBD_mut_escape_df.csv
RBD_mut_escape_df.csv
 
 
RBD_mut_escape_df.py
RBD_mut_escape_df.py
 
 
RBD_mutation_escape_fractions.csv
RBD_mutation_escape_fractions.csv
 
 
RBD_seq.fasta
RBD_seq.fasta
 
 
RBD_variants_escape_exact.csv
RBD_variants_escape_exact.csv
 
 
RBD_variants_escape_noisy.csv
RBD_variants_escape_noisy.csv
 
 
README.md
README.md
 
 
biophysical_model.ipynb
biophysical_model.ipynb
 
 
concentration_set.ipynb
concentration_set.ipynb
 
 
fit_2epitope.ipynb
fit_2epitope.ipynb
 
 
fit_RBD.ipynb
fit_RBD.ipynb
 
 
libA_220810_1_1C04-5G04_1_prob_escape.csv
libA_220810_1_1C04-5G04_1_prob_escape.csv
 
 
library_size.ipynb
library_size.ipynb
 
 
mutation_rate.ipynb
mutation_rate.ipynb
 
 
optimization.ipynb
optimization.ipynb
 
 
partition_function.ipynb
partition_function.ipynb
 
 
real_LyCoV1404.ipynb
real_LyCoV1404.ipynb
 
 
real_cocktail.ipynb
real_cocktail.ipynb
 
 
reference_site_numbering.ipynb
reference_site_numbering.ipynb
 
 
simulate_RBD.ipynb
simulate_RBD.ipynb
 
 
specify_epitopes.ipynb
specify_epitopes.ipynb
 
 
visualize_RBD.ipynb
visualize_RBD.ipynb
 
 

README.md

Jupyter notebooks

Jupyter notebooks demonstrating use of the package.

These are tested against their current results using nbval, and incorporated into the documentation using nbsphinx.

SARS-CoV-2 RBD data

These data are used for plausible simulated escape data against the RBD.

Data for antibodies targeting four "epitopes" on the SARS-CoV-2 RBD using the classification scheme of Barnes et al (2020):

  • LY-CoV016: a "class 1" epitope
  • LY-CoV555: a "class 2" epitope
  • REGN10987: a "class 3" epitope
  • CR3022: a "class 4" epitope

The file RBD_mutation_escape_fractions.csv contains the mutation-level escape fractions for each antibody measured using deep mutational scanning in the following papers, only including mutations for which measurements are available for all four antibodies:

The file RBD_mut_escape_df.csv contains mutation escape values (the "beta" values for the polyclonal package) generated from the mutation-level escape fractions using the script RBD_mut_escape_df.py.

The file RBD_activity_wt_df.csv contains the activity values for each epitope used in the simulations.

The file RBD_seq.fasta is the coding sequence of the RBD used in the Bloom lab deep mutational scanning (optimized for yeast display).

The directory also contains 6M0J.pdb, which is just a downloaded version of PDB 6m0j, which has the RBD in complex with ACE2.

SARS-CoV-2 spike data

These are real data from deep mutational scanning: