PDB SMILES Query

THIS NODE NO LONGER WORKS AS THE REMOTE WEBSERVICE HAS BEEN SHUTDOWN

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