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Glide Ensemble Docking

DeprecatedDeprecated Nodes version 21.1.156.202102141445 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.
Note: If the option to write XP descriptor information is selected, the file(s) 'XPDES_jobID_gridNo.xpdes' will be saved in the temporary directory.

Backend implementation

$SCHRODINGER/glide

Constraints

Currently this node supports "h-bond", "metal" 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.

Input Ports

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Glide Grid
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Ligands in Maestro or SD format

Output Ports

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Pose Viewer (i.e Receptor and docked ligands)
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Receptor in Maestro format
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Docked ligands in Maestro format

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 4.3

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Developers

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