Assess Affinity with Hyde in SeeSAR

This node assesses the affinity of a protein-ligand complex with Hyde in SeeSAR, given a library table with molecules in sdf or mol2 format, and a protein table with entries in pdb format. The SeeSAR-Hyde score and the assessment details will be sent to the output port.

SeeSAR has to be licensed separately, see http://www.biosolveit.de/SeeSAR/ for more details.

Options

Library column

The molecules provided in this column are assessed with Hyde in SeeSAR. If the input table contains more than one column with a compatible type, you can choose here which column should be taken. The molecules have to be 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 in SeeSAR and will be rejected.

Reference ligand column

The Binding Site will be defined by this reference ligand molecule.
The first molecule will be taken, in case there are more than one.

Protein column

Name of the column containing the protein description in pdb format.

Threshold for the minimum required activity [nM]

SeeSAR will only output poses with an estimated activity below this threshold. The value is given in nM. If entered value equals 0.0 (the default), no threshold will be set.

Append all data columns of the library table

Select this if you want to append all additional data columns of your input table to the output table.

Keep debug files and show the log after the run

This setting keeps all temporary files and opens an editor to show the output of the external program. This setting is very helpful for debugging.

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 in SeeSAR 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 pdb will be ignored.

SeeSAR Project: The project defined by the SeeSAR node.
Reference ligand and protein will be ignored, if project is given.

Output Ports

SeeSAR Project: The SeeSAR project file with all pre-calculated Hyde scores.

Results: The SeeSAR-Hyde scoring results. The table contains the poses written by SeeSAR and the affinity ranges estimated by Hyde in SeeSAR. The output molecules are always written in sdf format regardless of the format of the given input.

Errors: The rows of the incoming table which could not be assessed by SeeSAR for any reason.

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Installation

To use this node in KNIME, install BioSolveIT SeeSAR for Knime from the following update site: