0 ×

PDB Describe Heterogens

Vernalis PDB Connector KNIME nodes package version 1.30.2.v202106181332 by Vernalis (R&D), UK

This node uses the PDB ( www.rcsb.org ) " Describe Chemical Components " webservice to provide details of chemical components ("heterogens") identified by their 1 - 3 character PDB Het ID. The service does not provide results for standard proteinergic L-amino acids.

The PDB Describe Heterogens node was developed by Vernalis (Cambridge, UK) . For feedback and more information, please contact knime@vernalis.com


Search Options

Het ID Column
Select a string column containing the 1 - 3 Character heterogen IDs. The querying is case-insensitive.
Heterogen Type
Add the heterogen type - e.g. 'D-peptide linking', 'non-polymer' etc. NB Standard amino acid residues, e.g. SER are not returned by this service, but modified and non-standard residues, e.g. SEP are returned.
Molecular Weight
Add the Molecular Weight
Chemical Name
Add the chemical name
Add the formula
InChI Key
Add the InChI Key
Add the InChI string
Add the SMILES string

Connection Properties

Maximum URL Length
The maximum length of the URL submitted to the GET webservice (2000 - 8000 characters). Higher values will result in fewer calls to the service, but may be blocked by proxy servers.

Input Ports

Input table containing a column of PDB Heterogen IDs

Output Ports

The input table, with selected heterogen information added

Best Friends (Incoming)

Best Friends (Outgoing)


To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:


A zipped version of the software site can be downloaded here.

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.