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Glide One Step Docking

DeprecatedDeprecated Nodes version 21.1.156.202102141445 by Schrödinger

This node performs the Glide grid generation and ligand docking. Settings for Glide are made in this section. If multiple receptors are specified in the input data, the settings are applied to each receptor. This means that the binding site is defined by the same residue specifications for each receptor. For example, if a ligand is used, it must have the same residue name, residue number, and chain ID in each complex.

Backend implementation

scripts/ifd/glide-dockingCLI.py
The script glide-dockingCLI.py is used to implement this node.

Options

Binding Site
Grid center. The center can be specified in one of the following ways:

coords x,y,z

ligand residue-spec

residues residue-spec,residue-spec,...

('residue-spec' should be defined as <Chain ID>:<residue name><residue number>, in case residue is not attached to chain, <Chain ID> should be defined as '_')

where,
coords - specifies the grid center directly
ligand - specifies the centroid of the ligand.
residues - specifies the centroid of the listed residues.

Ligands to dock
List of ligands to dock from the ligand input table. Can take the values all or self (ligand that was last docked with this receptor). The default is "all" for initial docking and should be changed to "self" for redocking.
Size [A]
Dimension of grid enclosing box. Can take the value auto or a number. The value auto computes the box size from the size of the ligand, if the grid is centered on the ligand, or sets it to 26 A if the grid is centered on the centroid of a set of residues.
Receptor vdW scaling
Scaling factor for receptor van der Waals radii.
Ligand vdW scaling
Scaling factor for ligand van der Waals radii.
Reject poses if Coulomb-van der Waals energy is greater than
The default is 100.0 for initial docking and should be changed to 0.0 for redocking.
Reject poses if hydrogen bonding energy is greater than
The default is -0.05 for initial docking and should be changed to 0.0 for redocking.
Redock without H-bond filtering if number of poses found is less than
The default is 1 for initial docking and should be changed to 0 for redocking.
Maximum number of poses per ligand
Maximum number of poses per ligand
Glide Type
Glide docking precision. Can take the values SP or XP.
Generate 4 additional conformations for input to Glide docking
These extra conformations improve the ligand pose. This option is unchecked by default, for initial docking and should be checked for redocking.

Input Ports

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Protein Structures in Maestro format
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Ligands in Maestro format

Output Ports

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Complex structures in Maestro format

Views

Log output of glide-dockingCLI.py
Log output of glide-dockingCLI.py

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.3

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Developers

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