Contents

This repository contains protein complex structures containing SARS-CoV-2 spike protein as well as derived data.

Important files:

• pdb/ACE2/complexes/*.pdb – SARS-CoV-2 complexes with ACE2 protein

  • pdb/ACE2/complexes/clusters/clusters.lst – file listing clusters based on contacts (epitopes), one cluster per line;
  • pdb/ACE2/complexes/clusters/contacts-..tab – TSV file listing averaged contact distances for each of the clusters (columns); lines correspond to aminoacid positions in SARS-CoV-2 spike glycoprotein; question marks (?) mark absent contacts for the position in question;
  • pdb/ACE2/complexes/contact-maps/distances/..tab – TSV file listing all complexes (columns) and their contacts (lines); lines correspond to aminoacid positions in SARS-CoV-2 spike glycoprotein; question marks (?) mark absent contacts for the position in question;
  • pdb/ACE2/complexes/dist-matrices/contact.m – distance matrix between complexes;

• pdb/antibodies/complexes/*.pdb – SARS-CoV-2 complexes with antibodies

  • pdb/antibodies/complexes/clusters/clusters.lst – file listing clusters based on contacts (epitopes), one cluster per line;
  • pdb/antibodies/complexes/clusters/contacts-..tab – TSV file listing averaged contact distances for each of the clusters (columns); lines correspond to aminoacid positions in SARS-CoV-2 spike glycoprotein; question marks (?) mark absent contacts for the position in question;
  • pdb/antibodies/complexes/contact-maps/distances/..tab – TSV file listing all complexes (columns) and their contacts (lines); lines correspond to aminoacid positions in SARS-CoV-2 spike glycoprotein; question marks (?) mark absent contacts for the position in question;
  • pdb/antibodies/complexes/dist-matrices/contact.m – distance matrix between complexes;

• pdb/pristine/*.pdb – original PDB files as downloaded from the Protein DataBank

Acknowledgments

This project has received funding from European Regional Development Fund (project No 13.1.1-LMT-K-718-05-0023) under grant agreement with the Research Council of Lithuania (LMTLT). Funded as European Union's measure in response to Cov-19 pandemic.