Downloading PDB files from BindingDB by script
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Entering edit mode
3.4 years ago

Hello everyone,

I am trying to find a way to download PDB files of a proteins that have co-crystalized ligand by using BindingDB. So, I have a file of BindingDB IDS, and I want for each ID to download pdb files for each ligand that binds to that protein. Previously I was using a script to download directly specific PDB files from RSCB: PDB, but now I have to do the same, but I have BindingDB IDs.

Previous script that I've used looks like this:

#! usr/bin/perl -w

open (NDX, 'file.txt');
@ndx_ar = <NDX>;
close NDX;
$ndx_sz = scalar@ndx_ar;
for ($c = 0; $c < $ndx_sz; ++$c)
{
     chomp $ndx_ar[$c];
     if ($ndx_ar[$c] =~ /pdb/)
     {
      $ndx_ar[$c] =~ s/.pdb//;
      `wget 'http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=$ndx_ar[$c]' -O $ndx_ar[$c].pdb`;
     }
     else
     {
      `wget 'http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=$ndx_ar[$c]' -O $ndx_ar[$c].pdb`;
     }
}

exit;

Maybe some other way to download these data exists, but I couldn't find it so far.

Many thanks!

perl • 1.1k views
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