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PDB Downloader

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

This node, and the corresponding source node, allows the downloading of structure and sequence files from the RCSB PDB. The formats supported are:
  • PDB
  • mmCIF
  • Structure Factors
  • FASTA Format Sequence
PDB files are cast as PDB cells, and PDBML as XML cells. No checking the the structure IDs is carried out - invalid IDs will return cells containing missing values. WARNING - the PDBx option can result in very large tables!

This node was developed by Vernalis (Cambridge, UK). For feedback and more information, please contact knime@vernalis.com


Select a column containing the PDB IDs
Select a String column containing a list of PDB IDs
Download formats
Select the desired file format(s) from the available options - PDB, mmCIF, Structure Factors, PDBML/XML (PDBx), FASTA Sequence

Input Ports

Input Data table contaning a list of PDB IDs

Output Ports

Output table with downloaded file(s) appended

Best Friends (Incoming)

Best Friends (Outgoing)



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