PDB Describe Heterogens

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

Options

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
Formula: Add the formula
InChI Key: Add the InChI Key
InChI: Add the InChI string
SMILES: 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

Popular Predecessors

Popular Successors

Views

This node has no views

Workflows

Developers

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.

Installation

To use this node in KNIME, install the extension Vernalis KNIME Nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.4

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

Plugin provider: Vernalis Research, UK

Plugin version: 1.37.0.v202412091759

On NodePit since: 2024-12-06

Last update: 2024-12-30

KNIME versions: v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!