PDB Chemical Structure Search

This component performs a query for chemical structure searches using the SMILES notation. The component is based on the RCSB PDB RESTful WebServices.

The chemical structure search query results in a list of PDB IDs and the associated ligand information (chemicalID). Additionally information like chemical name, smiles, molecular weight, formula, InChiKey and InChI of the respective ligand is provided. The output table also includes, a column with combined score of results from different services (sequence, seqmotif, strucmotif, structure, chemical, and text) and results are sorted in decreasing order of this score.

The following search types are possible with the component:
• graph-strict
• graph-relaxed
• graph-relaxed-stereo
• fingerprint-similarity

Documentation about the RESTful WebService from PDB can be found here:
https://search.rcsb.org/index.html#search-services

General information about the RCSB PDB database can be found here:
https://academic.oup.com/nar/article/28/1/235/2384399

Output ports

1. Type: Table
   Output port
   Output table contains information about protein structures and their ligands that matched the search query.