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Protein Preparation Constrained Refinement

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 Protein Refinement does a constrained minimization of the protein. Its main purpose is to relax the hydrogens.

Backend implementation

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

Options

RMSD value: This value specifies the convergence threshold for the constrained minimization of the Glide protein preparation. The minimization ends when the RMSD is less than or equal to value.

Input Ports

: Protein Structure in Maestro format

Output Ports

: Minimized Protein Structure in Maestro format

Popular Predecessors

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Views

Log output of pprepCLI.py: Log output of pprepCLI.py

Workflows

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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: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-11-20

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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