PDB Downloader

This Node Is Deprecated — This version of the node has been replaced with a new and improved version. The old version is kept for backwards-compatibility, but for all new workflows we suggest to use the version linked below.
Go to Suggested ReplacementPDB Downloader
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


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