Proteax® KNIME™ node examples
This page lists a number of KNIME workflows that demonstrates some of the capabilities of the Proteax KNIME nodes. Each workflow can be downloaded as a ZIP file (click the link below the workflow graphic) and then imported into your own KNIME installation by using KNIME's "Import KNIME workflow..." command from the File menu, which brings up the dialog shown below.
Choose "Select archive file" and browse to the downloaded workflow ZIP file.
Simple report of protein properties
A workflow that contains some well-known proteins described in PLN (Protein Line Notation) format. The workflow assumes that you have the KNIME reporting tool installed. If you do not have the KNIME reporting tool installed, you may just delete the report node and look at the data produced by the final Proteax node.
PLN report demo (40 kB)
Protein SAR table - insulin analogs
Protein SAR tables produced by Proteax's DerNot expressions. Like the example above, it assumes that you have the KNIME reporting tool installed, but it can be used without.
Protein SAR table demo (42 kB)
Protein SAR table - cyclic peptides
Another SAR table demo - only with cyclic peptides to demonstrate Proteax's ability to handle cyclic mis-alignments robustly.
Structure to sequence conversion
Proteax is able to convert chemical structures into Protein Line Notation. This workflow shows a number of oxytocin variants downloaded from PubChem which are then converted to PLN. The workflow then lets you compare the input structures with the calculated sequences and structures re-constructed from sequence.
You need to have the basic chemistry extensions installed to use the workflow. To view the structures it is highly recommended to also install the Marvin or Indigo nodes so KNIME can render SDF cells directly when you view output port data.
Structure to sequence conversion - with structures displayed by ChemAxon Marvin nodes
A slight variation on the above workflow that uses the ChemAxon Marvin nodes to display chemical structures. This means that you need to have the free Marvin nodes installed to use this workflow.
Peptide structure to sequence demo - with Marvin nodes (50 kB)
Input SD file for the workflow (81 kB - same input SD file as the above workflow)