This node takes a protein and a reference molecule to define a
binding site. Molecules from the input table are docked with
FlexX into this binding site. Alternatively, if a template
molecule is provided, those molecules are overlayed onto the
template based on the maximum common substructure (MCS) and
scored using the FlexX-scoring function. The solutions with the
best scores are written to the output table. Molecules that cannot
be docked for whatever reason, are written to the error table.
You may also define your docking with the SeeSAR Interactive
node. Besides the binding site you will be able to define
pharmacophore constraints for your docking results.
FlexX has to be licensed separately, see
http://www.biosolveit.de/FlexX/ for more details.
Options
Input Ports
- Library: Input table with molecules in sdf or mol2 format with 3d coordinates.
- Reference Ligand: Input table with a binding site defining molecule in sdf or mol2 format with 3d coordinates. In case of multiple entries, only the first one will be taken.
- PDB: Input table with a protein column in pdb format.
- Template Pose: Input table with a template molecule in sdf or mol2 format with 3d coordinates. In case of multiple entries, only the first one will be taken.
- SeeSAR Project: Reference ligand and protein will be ignored,
if a project is available.
Popular Predecessors
- 3D Coordinates Generator19 %
- SeeSAR Interactive GUI10 %
- SDF Reader7 %
- Mol2 Reader6 %
- SeeSAR Project Reader5 %
- PDB Loader4 %
Read PDB3 %- 3D Ensemble Conformator3 %
- MolConverter2 %
- Chunk Loop Start2 %
- Molecule Converter (Naomi)2 %
- Load Local PDB Files2 %
- Concatenate2 %
- Column Filter2 %
- PDB Downloader1 %
- Table Creator1 %
- Parallel Chunk End< 1 %
- Try (Data Ports)< 1 %
Column Rename< 1 %- PDB Reader< 1 %
Table Reader< 1 %- Row Filter< 1 %
- Chemical Space Searcher (FTrees)< 1 %
- Tautomer Generator (Naomi)< 1 %
- Reaction Space Generator< 1 %
- Induced Fit Docking< 1 %
- PDB Reader< 1 %
- Load Local Mol2 Files< 1 %
- Benchmark Start< 1 %
PDB Connector< 1 %- PDB Downloader (Source)< 1 %
- Duplicate Row Filter< 1 %
- Row Splitter< 1 %
- RowID< 1 %
- Molecule Type Cast< 1 %
- Parallel Chunk Start< 1 %
- OpenBabel< 1 %
- Integer Input (legacy)< 1 %
- Docking (FlexX)< 1 %
- String Manipulation< 1 %
- SDF Inserter< 1 %
- Integer Slider Configuration< 1 %
Views
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Workflows
Links
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Developers
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