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

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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:

v5.3

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

Plugin provider: Vernalis Research, UK

Plugin version: 1.36.7.v202405281205

On NodePit since: 2024-07-11

Last update: 2024-11-20

KNIME versions: 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

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