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Side Chain Remover

DeprecatedDeprecated Nodes version 21.1.156.202102141445 by Schrödinger

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

Views

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

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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