This node is currently not available in KNIME v5.9 — instead we’re showing this page for KNIME v5.2. You can use the version menu in the title bar to permanently switch your preferred version. This will also show the link to the update site.
This node assesses the affinity of a protein-ligand complex with
HYDE, given a library table with molecules in sdf or mol2
format, and a protein table with entries in pdb format.
The HYDE score and the assessment details will be sent to the
output port.
HYDE has to be licensed separately, see
https://www.biosolveit.de/HYDE for more details.
Options
Input Ports
- Library: Input table with molecules in sdf or mol2 format with 3d coordinates. Please note that the molecules have to be located within the Binding Site, otherwise they cannot be assessed with HYDE and will be rejected.
- Reference Ligand: Input table with molecules in
sdf or mol2 format with 3d coordinates. The first molecule of
the selected column will be used to define the Binding Site.
If a SeeSAR project is given, the reference ligand will be ignored. - PDB: Input table with a protein column in pdb format.
If a SeeSAR project is given, the protein will be ignored. 
- SeeSAR Project: Reference ligand and protein will be ignored, if a project is available.
Output Ports
- Results: The HYDE scoring results. The table contains the exported poses and the affinity ranges estimated by HYDE. The output molecules are always written in sdf format regardless of the format of the given input. All input columns will be appended.
- Errors: The rows of the incoming table which could not be assessed by HYDE for any reason.
Views
- This node has no views
Workflows
- No workflows found
Links
- No links available
Developers
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.