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pull out PDB binding data

I want to pull out residue and hetatom coordinates in PDB files and make an evaluation of what the contact residues are.

I then want to compare these residues against alignments. If these residues are conserved in an alignmet, star those residues. Reasons for doing this is that I have 15,000 rows of initial "hits" on a many-against-many alignment.

Can someone point me in the right direction on reading for this?

Mike
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  • You can do this using most languages of your preference, but I'm not aware of any tool that does this by itself. You can certainly write a Python or R or Perl script that will do this though, by reading the PDB file, comparing data to your 15,000 rows, checking if it's conserved, then adding a "star" to the observations that hit – csgroen Aug 31 '20 at 10:44
  • Thank you so much; yes my intention is to start writing a script for this; Dresden has PLIP, which does this very well: https://projects.biotec.tu-dresden.de/ This proteome-wide screen is quite powerful, it is my hope to get it online with a nice user-friendly GUI – Mike Aug 31 '20 at 17:22
  • Depending on how much processing this requires, look into R's `shiny` framework. Very easy to deploy webapps with shiny :) – csgroen Sep 03 '20 at 13:49

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