Reading pdb files


Is there any tool in Knime that enables you to read pdb files? I’m using Knime version 2.0.2 and I haven’t been able to find any.

Thanks in advance for any help you can provide.

Hallo Sara.
Interesting comment. Thank you.
We are working on it in collaboration with Structure Biology group.
Please let us know what exactly are you expecting from PDB (which information should be transformed into table).

Best regards,

Hello Karol. Thanks for your answer.

The information we need the reader to extract from the PBD file at this moment is the protein and crystallized ligand coordinates.

Let me know if this make sense to you because I’m not an expert in the field.

Best regards,


The PDB type actually does already exist. We just did not find the time (as so often) to
implement nodes doing something useful with them. As usual in KNIME, we would not
want to interpret the files but instead leave the interpretation to the nodes processing
PDB cells and the KNIME PDBCells only holding the textual representation. That way the
user always sees when a potential information loss can happen because all conversions
are made explicit in the flow.

Sara, it sounds as if you have a node doing something with PDBs? Are you using our
type already or did you implement your own?