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Induced Fit Docking

DeprecatedDeprecated Nodes version 21.1.156.202102141445 by Schrödinger

This node allows one to set up a sequence of jobs in which ligands are docked with Glide, then Prime Refinement is used to allow the receptor to relax, and the ligands are redocked into the relaxed receptor with Glide.

Backend implementation

scripts/ifd/ifdCLI.py
The script ifdCLI.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.

# Prime CPUs
# Glide CPUs
Box Size
Dimension of grid enclosing box. Can choose the value auto or a number. 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.
Protein Prep constrained refinement
Constraint of pre-minimization
Remove side chains of residues
ASL expression to specify the residues whose side chains should be temporarily removed by mutating the residues to alanine. The sidechain label is not changed and will be used later by the Induced Fit node to repredict the original residue. This option is optional and only added when the check box is selected.
Receptor vdW scaling
Scaling factor for receptor van der Waals radii.
Ligand vdW scaling
Scaling factor for ligand van der Waals radii.
# Poses
Maximum number of poses per ligand
Refine residues within ... A of ligand poses
Distance cutoff
Precision
Glide docking precision. Can choose the values SP or XP.

Input Ports

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Receptor or Complex structures in Maestro format
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Ligands in Maestro format

Output Ports

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Complex structures in Maestro format ranked by IFD Score

Views

Log output of IFD
Log output of IFD
IFD StdOutErr View
Std output/error of IFD

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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