Affinity Calculator (HYDE)

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

Library column
The molecules provided in this column are assessed with HYDE. 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 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.
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

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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.
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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.
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PDB: Input table with a protein column in pdb format.
If a SeeSAR project is given, the protein will be ignored.
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SeeSAR Project: Reference ligand and protein will be ignored, if a project is available.

Output Ports

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

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