0 ×

PDB Connector Query Only

Vernalis PDB Connector KNIME nodes package version 1.27.0.v202008190633 by Vernalis (R&D), UK

The PDB Connector Query Only source node provides connections to the RESTful Web Service for searching for information from the Protein Data Bank at http://www.rcsb.org/pdb/rest/search

The user interface dialog options are designed to be a close mimic of the interactive web-based search and reporting options provided at http://www.pdb.org/pdb/search/advSearch.do and the user is encouraged to explore this resource for a full explanation of each search option. Alternatively, use the PDB Connector Query only (XML Query) node to paste an XML query directly from the "Query Details" link in the query results pages on the PDB page. The XML Query is made available as a flow variable ( xmlQuery ) after node execution.

The PDB Connector Query Only 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)
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

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


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

Best Friends (Incoming)

Best Friends (Outgoing)


To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.