How to retrieve PDB-complex codes from PDB-ligand code?

Dear KNIME-vernalis nodes users,

I’m using the RCSB PDB Tools package to extract information about PDB entries and I think these nodes are a great addition to KNIME community extension.

I came up with a pretty common need: I would like to extract for a certain ligand of which I have a PDB-code, the list of all the PDB-complexes codes in which the ligand appears. Is this possible using RCSB PDB Tools package?
If this is not possible, do you know how can this can be done using RCSB-PDB and KNIME Web Service nodes?

Thanks in advance for any help!

Gio

1 Like

It is possible, although it isn’t entirely obvious how to do it. The attached workflow shows the solution. The main point is that if you use the PDB Connector (Query Only) node:

and dig around deep in the Flow Variables tab, then you can set the Ligand ID to come in from a flow variable:

having enabed that option in the ‘Chemical Components’ tab:

RCSB PDB Component lookup.knwf (16.9 KB)

Hope that helps,

Steve

3 Likes

Hi Steve,
Thank you very much for the detailed information. That’s great!
I didn’t realized how to do that with the PDB Connector Query Only node. I hope this post will help also other users who try to do that.
Cheers,
Gio

1 Like

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.