This node is currently not available in KNIME v5.4 — instead we’re showing this page for KNIME v5.2. You can use the version menu in the title bar to permanently switch your preferred version. This will also show the link to the update site.

Glide Ligand Docking

This Node Is Deprecated — This version of the node has been replaced with a new and improved version. The old version is kept for backwards-compatibility, but for all new workflows we suggest to use the version linked below.

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

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

Output Ports

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

Popular Predecessors

Popular Successors

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

Workflows

Molecular fragments recommendation systemNodePit Space

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.

Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-12-18

Tags: Deprecated

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!