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

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Complex structures in Maestro format

Output Ports

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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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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: 2024-04-19
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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