Analysis of SARS-CoV-2 RBD antibodies encoded by IGHV2-5/IGLV2-14

Dependencies

• python3
• Igblast
• PyIR
• BioPython
• Pandas
• Openpyxl
• R

Dependencies Installation

Install dependencies by conda:

conda create -n Abs -c bioconda -c anaconda -c conda-forge \
  python=3.9 \
  biopython \
  pandas \
  openpyxl \
  igblast

Input files

• ./data/neut.tsv: pseudovirus neutralization data (IC50) from literature
• ./data/cAb_donor_info.xlsx: meta-information about antibody repertoire data for healthy donors
• ./data/HV_2-5_freq.tsv: summary ofIGHV2-5 allele frequency in RBD antibodies and in antibody repertoire data

Calculate the frequency of different IGHV2-5 alleles

1. Download antibody repertoire data for healthy donors from cAb-Rep

2. Calculate the frequency of different IGHV2-5 alleles in healthy donors
   python3 code/Cal_repertoire_freq.py

Plotting

1. Plot neutralization data of IGHV2-5/IGLV2-14-encoded RBD antibodies that are collected from literature
   Rscript code/neut_heatmap.R

2. Plot IGHV2-5 allele frequency in IGHV2-5/IGLV2-14-encoded RBD antibodies and in antibody repertoire data Rscript code/plot_allele.R

ddG calculation

See README file in rosetta_simulation