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Glide Ligand Docking

DeprecatedDeprecated Nodes version 20.3.139.202008120556 by Schrödinger

Ligand Docking uses Glide to dock ligands into existing grids. The docking calculations can be carried out in either Standard Precision (SP), Extra Precision (XP), or High-throughput Virtual Screening (HTVS) mode.
Note1: If the option to write XP descriptor information is selected, the file 'XPDES_jobID.xpdes' will be saved in the temporary directory.
Note2: Always use ungrouped Ligands as input if "Input plus Output" or "Output replaces Input" is selected, so that the output is matched with the input properly.

Backend implementation

$SCHRODINGER/run glide_sif.py and $SCHRODINGER/glide
glide_sif.py is used to write the input file. The command line tool glide is used to implement this node.

Constraints

Currently this node supports "h-bond" and "positional" constraints, which can be selected under the "Constraints" tab. Positional constraints must include a "custom" feature type specifying the SMARTS patterns and the list of atoms that must satisfy the constraint. This can be provided by selecting the feature details cell for the constraint in question. An additional window will open, where the user can either select a text file containing the smarts patterns and atom numbers or manually enter them in a text area. Each smarts pattern should be entered on separate lines using "<SMARTS PATTERN> <ATOM1,ATOM2..>", for example:
[N;X2]=C[N;X3] 1
[O;X1]~[N;X3]~[O;X1] 1,3
Multiple atoms can be specified for each pattern, but only one of the specified atoms is constrained. Normally, only one atom should be specified, to ensure that the correct atom is constrained. However, if the functional group contains multiple acceptors or donors, for example, you can specify all of them if you want any one of them to be constrained. This is not necessary for groups such as carboxylates, where the local symmetry of the functional group is used and either of the oxygen atoms in the carboxylate can be selected for the constraint, even though only one of them is specified.

Options

Output Column Structure
Output column

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Extract properties
Extract the Glide properties and add them as separate columns in the output table. [Primary, All, None]
Add origin columns
If checked ON, adds Origin Directory, Grid Prefix and Origin Hostname columns to the output table
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: GlideLigandDocking
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option from command line, just specify the option_name and the value as _off_ through the flow variable.

Input Ports

Icon
Glide Grid
Icon
Ligands in Maestro, Sd or Mol2 format

Output Ports

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Pose Viewer in Maestro or Sd format (i.e Receptor and docked ligands or only ligands)

Views

Score output of Ligand Docking
Score output of Ligand Docking
Log output of Ligand Docking
Glide Log File
Report output of GLIDE Ligand Docking
Report output of GLIDE Ligand Docking

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.2
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Developers

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