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

This node queries the PDB (www.rcsb.org) webservice described briefly here. The query accepts a SMILES or SMARTS query string, and can perform a variety of query types:

  • Exact Match
  • Substructure
  • Superstructure
  • Similarity
If the Similarity option is selected, then the threshold value is enabled and used in the query.

The SMILES string is only validated by sending it to the service - if the service is unable to correctly interpret the supplied string, then an execution error will result. The service will return a list of chemical components, along with all the structures each component is found in, and a number of details about the chemical component(s), as specified in the node dialogue. The second and third output tables provide a sorted list of the chemical component and structure IDs respectively.

NOTE Queries are sent un-encrypted to the service, and so could be intercepted by 3rd parties.

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


The SMILES String to be queried. SMARTS strings are also accepted for appropriate query types
Select Query Type
Select the required structure query type
Similarity Threshold
The similarity threshold for similarity queries in range 0.0 (least similar) to 1.0 (most similar)
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

Output Ports

Output table containing at the very least a list of all the Heterogen ID:Structure ID pairs found for ligands matching the query entered, plus additional columns relating to the ligand properties
A list of the ligand IDs matching the query entered
A list of the structure IDs containing ligands matching the query entered

Best Friends (Incoming)

Best Friends (Outgoing)



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