SeeSAR Project Generator

Setup your protein with SeeSAR. Your definition of a Binding Site will be stored in a SeeSAR project, that serves as input for Hyde with SeeSAR or FlexX docking.

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

Options

Molecule column: Molecules from this column will be imported into SeeSAR's analyzer table.
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: The first protein provided in this column is loaded into SeeSAR. If the input table contains more than one column with a compatible type (PDB), you can choose here which column should be taken.
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 SeeSAR. This setting is useful for debugging.

Input Ports

: Library: Input table with molecules in sdf, smiles or mol2 format.
: 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.
: PDB: Input table with a protein column in pdb format.

Output Ports

: SeeSAR Project: The SeeSAR project with the Binding Site defined based on the given PDB and reference ligand.
After having run this node, a tooltip on this port will indicate, whether a docking is defined or not. If a docking is present, it will show "(with defined docking)", which is necessary to use it as input for the FlexX docking node.

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Installation

To use this node in KNIME, install the extension BioSolveIT SeeSAR for Knime from the below update site following our NodePit Product and Node Installation Guide:

v5.2

Plugin provider: BioSolveIT GmbH

Plugin version: 2.29.3.202309291626

On NodePit since: 2023-12-06

Last update: 2024-05-08

KNIME versions: Since v3.6

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