Help - Bio.PDB - Find similar structures based on metal interactions

Question

[bsa4]

Hi,

I'm struggling with the writing of a script to search PDB files with a similar heteroatom interactions.

I have some reference structures where Mn interacts with a ligand (2 or 3 interactions, usually with 2 O, sometimes with a N too), GLU (1 interaction with O), GLU (1 or 2 interactions, both with O), and ASP (1 interaction with O). Examples of these reference structures are PDB ID 3wqq and 4kp7.

So, the idea was to search for structures in the PDB database that also have these interactions, using the distances or not (if possible).

But, as I see it, I have to start with the information about the Mn and this is already a problem.

I was trying to do something using the Bio.PDB.Selection.unfold_entities and NeighborSearch, but I got almost no progress so far.

As a beginner in python, and coding in general, do you have any ideas of a script for me?

At this point, any help is more than welcomed.

[bsa4]

Thanks, Mensur.

I'll take a look.

Answer 1

[Mensur Dlakic]

There is a suite of programs at Uppsala Software Factory that may be helpful. Their manuals can be found here. I recommend that you skim through all of them, but SPASM, RIGOR and SAVANT are probably most appropriate for your needs.