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ComponentComponent

PDB Chemical Structure Search

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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

Component details

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

Used extensions & nodes

Created with KNIME Analytics Platform version 4.3.1
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    KNIME Javasnippet Trusted extension

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    KNIME JSON-Processing Trusted extension

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    KNIME Quick Forms Trusted extension

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    KNIME REST Client Extension Trusted extension

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