0 ×

PDB Downloader

StreamableVernalis PDB Connector KNIME nodes package version 1.30.2.v202106181332 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 (not all formats are available for all structures!):
  • PDB
  • mmCIF
  • Structure Factors
  • FASTA Format Sequence
  • NMR Restraints
  • NMR Restraints v2
  • NMR Chemical Shifts
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 PDBML 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
Downloaded Files
Select the desired file format(s) from the available options
Select All
Selects all options in the Downloaded Files option list
Clears the selection and returns it to the default (PDB only) selection

Input Ports

Input Data table containing a list of PDB IDs

Output Ports

Output table with downloaded file(s) appended

Best Friends (Incoming)

Best Friends (Outgoing)



To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:


You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.