PDB SMILES Query
StreamableVernalis PDB Connector KNIME nodes package version 1.28.0.v202012181340 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
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
Options
- SMILES Query
- 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
- Formula
- Add the formula
- InChI Key
- Add the InChI Key
- InChI
- Add the InChI string
- SMILES
- 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)
Table Row to Variable(40 %) DeprecatedTable Row To Variable Loop Start(33 %) DeprecatedTable Column to Variable(13 %) Deprecated- Double Input (7 %)
Table Row to Variable(7 %) Deprecated
Best Friends (Outgoing)
- Loop End (19 %)
- Loop End (3 ports) (10 %)
- Fragment information (10 %)
- Speedy SMILES Possible Stereoisomer Count (5 %) Streamable
- Speedy SMILES De-salt (5 %) Streamable
- Show all 16 recommendations
Workflows
Related PDB structures (KNIME Hub) - Related PDB structures (KNIME Hub)
- Related PDB structures (Schrödinger)
- Related PDB structures (KNIME Hub)
- Related PDB structures (Schrödinger)
Installation
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.
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Developers
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