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PDB Connector

DeprecatedVernalis PDB Connector KNIME nodes package version 1.30.2.v202105121103 by Vernalis (R&D), UK

This node is no longer functional due to the shutdown of the remote webservices - Please use the new 'PDB Connector Query Builder' node instead

The new PDB Connector node was developed by Vernalis (Cambridge, UK) , based on the original PDB Connector node developed by Enspiral Discovery in collaboration with Vernalis (Cambridge, UK) . For feedback and more information, please contact knime@vernalis.com


Query Options

Remove Similar Sequences
Control the (optional) sequence similarity filter, used to remove similar sequences from the search hits.
Match multiple query terms using
Control the composite query logic (individual query options can be either ANDed or ORed together)
Ligand Image Size
Select the ligand image size to use in the generation of ligand image URLs (applies to Ligand Image field only).
Use POST Query method (Faster)
Select the POST or GET service. GET is older, but may limit number of report fields which can be returned, and is slower.
Max. Report request size
If using the GET option, the maximum URL length can be set between 2000 and 8000. Higher values allow more fields to be returned, and result in fewer calls to the webservice, but may fall foul of proxy servers. For POST request, longer requests can be sent, but may exceed an internal limit on the remote server or use too much memory
Clear Query
Clear all query options
Test Query
Test the current query, with display of xml query string and result count. NB The 'Test' button uses the query configured in the dialog, without reference to flow variable settings.
Messages relating to the Test Query button are displayed in this area
XML Query string
The xml query string generated from the user settings is displayed here when the 'Test' button has been pressed

Report Options

Select report
Use the dropdown menu to select from a number of predefined standard reports. Select 'Customizable Table' to allow fine-grained selection of all custom report fields, using the individual and group field selectors.
Select All
Initialise a Customizable Table with all report fields.
Clear All
Initialise a Customizable Table with no report fields.

Other query option tabs

To select a query option, either check the "Selected" checkbox or click anywhere on one of the individual query parameters. To unselect a query option, uncheck the "Selected" checkbox.
Enter values for the query term in the box(es) provided

Output Ports

One-column table of PDB IDs that match query
Custom report fields.


XML Query
A view of the combined XML Query
Logical Query
A 'logical' view of the combined Query

Best Friends (Incoming)

Best Friends (Outgoing)



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