KNIME node interface to _dockProjPrep script


Receptor PDB code or file name
Type a PDB code or choose file with receptor (pdb,icb)
Ligand Name
Select a ligand molecule. The ligand will be removed and the pocket used for docking
Box margin
Pocket box margin. Increase or decrease the value to adjust the binding pocket site.
Keep water
Option to keep water molecules.
Optimize Hydrogen
For PDB or non-ICM objects this option will toggle hydrogen optimization during the conversion.
Covalent Docking
Enables covalent docking section
Covalent Residue
Select a residue for the covalent attachement
Covalent Reaction
Select a file with the covalent reaction or use the default set.
Use All Reactions
If this option is selected all listed reaction will be tried. Otherwise use needs to manually pick a reaction from the list

Input Ports

This node has no input ports

Output Ports

Docking project path for MolIcmDockNode

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