Induced Fit Docking

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

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.

Views

Log output of IFD

Log output of IFD

IFD StdOutErr View

Std output/error of IFD

Workflows

• No workflows found

Links

• No links available

Developers