PDB Query and download

This workflow demonstrates using the newer PDBConnector nodes including the query builder and custom reporter, in conjunction with the PDB Downloader nodes to download and save local copies


This is a companion discussion topic for the original entry at https://kni.me/w/ICEaU_OO91c0fqTx

Hi,
I know these nodes are deprecated now as the remote webservices have been permanently shutdown.
I would like to know how to generate an output similar to the output of the former PDB custom report, to have data like UniprotID, Pfam accession code for each chain.
Thank you
Emilie

Hello @Emilie_Pihan,

when commenting on Hub workflow it’s always good idea to tag workflow creator like this @Vernalis :wink:

Br,
Ivan

3 Likes

I will keep this in mind!
Thank you
Emilie

2 Likes

HI Emilie,

You can still run the queries using the new PDB Connector nodes (unfortunately you will need to rebuild the queries you want as the new query api was not in any way backwards compatible).

Unfortunately, we are still working on a replacement for the custom reporting node. We have also used internally the PDBe restful interface (see PDBe REST API < PDBe < EMBL-EBI) using either the GET or POST nodes in KNIME, or using some custom in-house nodes using the PDBe RESTful API. We do also plan to release those at some point, but at the moment that’s not possible as we are working on rewriting them to use some of the standard JSON parsing libraries available in KNIME, which were not present when they were first written. In particular, it looks like the data you rare looking for are available under the SIFTS tab (direct link is PDBe REST API < PDBe < EMBL-EBI)

Steve

1 Like