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:
%%00009• graph-strict
%%00009• graph-relaxed
%%00009• graph-relaxed-stereo
%%00009• 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

Options

Maximum number of best matches: The maximum number of best hit records to fetch. Ignored if “Display All Results” is selected. Large numbers could result in slow execution.
Search types: Search types include graph-strict, graph-relaxed, graph-relaxed-stereo and fingerprint-similarity.
Results list: Defines if only a fixed number of results should be fetched and displayed or all possible results should be displayed. Selecting “Display All Results” could result in a long execution time depending the number of matches found according to the search configuration.
Enter a chemical structure using SMILES: This query performs chemical structure searches using the SMILES notation.

Input Ports

This node has no input ports

Output Ports

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

PDB Chemical Structure Search

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Input Ports

Output Ports

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