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SeeSAR Project Generator

BioSolveIT SeeSAR for Knime version 2.19.1.202102051628 by BioSolveIT GmbH

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

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

Output Ports

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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.

Installation

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

KNIME 4.3

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Developers

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