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PDB Describe Heterogens

Vernalis PDB Connector KNIME nodes package version 1.17.3.v201808160901 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

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

Best Friends (Incoming)

Best Friends (Outgoing)

Update Site

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