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Prime 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 Induced Fit predict sidechains within a distance around the ligand.

Backend implementation

scripts/ifd/refine-binding-siteCLI.py
The script refine-binding-siteCLI.py is used to implement this node.

Options

Distance cutoff: Cutoff distance (in angstroms) from the ligand pose, within which residues that have any atoms are included in the refinement list.

Input Ports

: Complex structures in Maestro format

Output Ports

: Induced fit complex structures in Maestro format

Popular Predecessors

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Popular Successors

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Views

Log output of refine-binding-siteCLI.py: Log output of refine-binding-siteCLI.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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