Side Chain Remover

This Node Is Deprecated — This node is kept for backwards-compatibility, but the usage in new workflows is no longer recommended. The documentation below might contain more information.

The Side Chain Remover should be used to trim flexible side chains which might clash with the ligands to be docked. Consult the Induced Fit Docking User manual if you are unsure which side chains to trim.

Backend implementation

scripts/ifd/trimCLI.py
The script trimCLI.py is used to implement this node.

Options

Trim side chains of residues (ASL)
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.

Input Ports

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Protein Structure in Maestro format

Output Ports

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Protein Structure with trimmed sidechains in Maestro format

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Views

Log output of trimCLI.py
Log output of trimCLI.py

Workflows

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Links

Developers

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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: 24.1.135.v202402072122
On NodePit since: 2023-12-06
Last update: 2024-04-22
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

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