3D-e-Chem GPCRdb "Item could not be found on GPCRDB server"

#1

Hi guys,
I’m trying to use the GPCRDB Structure-ligand Interaction node from 3D-e-Chem package. This node takes as input a PDB code of a GPCR and it should output a list of protein-ligand interactions. Nevertheless when I try to run it, it always says me:

"Execute failed: Item could not be found on GPCRDB server".

I checked that the item I’m searching is present in the GPCRDB. As for example 4N6H. Does anybody know why this happens? How can I make it work?

Thanks in advance!

#2

Hi,

I am also getting not found errors.
I will try to resolve it.

Stefan

#3

Hi,

I have found the problem (the url for gprcrdb web services needed to be updated) and is fixed in 3D-e-Chem nodes v1.4.2 release . It should be available in a couple of hours.

GPCRDB nodes in existing workflows should be replaced with the updated ones.

Can you try the updated nodes?

Stefan

2 Likes
#4

Dear Stefan,
Thank you for your help! Of course I can try the updated nodes. Will those be available in the “KNIME Community Extensions (Experimental)” at http://update.knime.com/community-contributions/4.1 ?
Currently I see that the most updated version there is v.1.4.1 release. I’ll wait some more hours.
Thanks again

#5

Dear Stefan,
I can confirm you that with the v1.4.2 release the problem is solved.
Thank you very much!
Gio

1 Like
#6

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