NCBI-Spike-Ab-search

This code will get a list of PDB IDs for structures that contain antibodies bound to the Receptor Binding Domain from the SARS-CoV-2 spike protein. 
The data are from the protein sequence database.  These represent sequences from 3D protein structures.
The results are shown in four columns:  the protein seqeuence ID, the PDB ID, the Chain name, and the name of the chain
For example:  1864383146	6XE1_L	Chain L, CV30 Fab Kappa chain
Today - this query found 445 protein chains from 231 antibodies
Before running this code, you need to install Entrez Direct (EDirect).  I downloaded and installed EDirect by following the instructions on this page https://www.ncbi.nlm.nih.gov/books/NBK179288/

./esearch -db protein -query "protein_structure_direct[Filter] AND SARS-CoV-2 AND Antibody AND Neutralizing AND RBD NOT Mers" |./efetch -format docsum| ./xtract -pattern DocumentSummary -sep "|" -element Id Caption Title