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Embrace Minimization

Schrödinger extension for KNIME Workbench version 20.4.144.202011111133 by Schrödinger

Multi-Ligand Bimolecular Association with Energetics (eMBrAcE) is an automated mechanism that allows one to study the association of ligands with a receptor.

An eMBrAcE minimization is a type of multiple minimization in which each of the specified pre-positioned ligands is minimized, in turn, with the receptor. You can perform eMBrAcE minimization calculations in two modes: Interaction Mode, in which the interaction between each ligand and the substrate is studied, and Energy Difference Mode, in which energy changes upon association are estimated.

For details on the types of calculations that eMBrAce enables see the MacroModel documentation.

Depending on the configuration the output from an eMBrAce calculation can be:

  • complexes only
  • ligands only
  • receptor, ligands and complexes (only in Energy Difference mode)

Backend implementation

scripts/mmodCLI.py run by cmdRunner.py
The script mmodCLI.py is passed to cmdRunner.py to implement this node.

Input Ports

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Pose Viewer data table (receptor and ligands) in Maestro format

Output Ports

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Molecules in Maestro format

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.2

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Developers

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