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Flare Viewer

Cresset KNIME Nodes version 2.6.0.41359 by www.cresset-group.com

Launches Flare™ to view ligand and protein structures. Flare is a structure-based design tool for the visualization and analysis of protein-ligand complexes. Flare main features are:

  • Smart import and handling of protein-ligand complexes
  • Accurate and reliable protein preparation
  • Sequence alignment and superimposition
  • Protein interaction potentials
  • Electrostatic complementarity
  • Accurate docking using Lead Finder
  • Minimization of protein ligand complexes
  • 3D-RISM water analysis (using Cresset XED and AMBER FFs)
  • WaterSwap analysis – ligand and binding site energetics
  • The Flare Python API

This node wraps the Flare executable, which must be installed with a valid license for this node to work. If this is installed in the default location on Windows, then it should be found automatically. Otherwise, you must either set the 'Cresset Home' preference setting or the CRESSET_HOME environment variable to the base Cresset software install directory. You may also set the 'Flare Path' preference setting or the CRESSET_FLARE_EXE environment variable to point directly at the executable itself.

For more information visit www.cresset-group.com or contact us at support@cresset-group.com.

Options

Ports

Column containing (optional) ligands structures
The column in the input datatable containing the ligands to visualize.
Column containing (optional) protein structure
The column in the input datatable containing the proteins to visualize.
Role for the imported ligands
The input molecules will be imported into the chosen role.
Description
Insert an optional description for the role
Ligand / Protein Protonation State
  • Ask - When the node is run, you will be asked to choose the protonation state
  • Use input protonation state - Imports the molecules 'as-is'
  • Let Flare choose the protonation state - Re-assigns protonation state for all molecules at pH 7 according to the Cresset built-in set of rules.
  • Open a protein prep dialog: this option available only for proteins. The protein preparation dialog will be displayed when Flare is opened.

Input Ports

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Ligands to view, in SDF, PDB or Mol2 format.
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Protein to view, in SDF, PDB or Mol2 format.

Workflows

Installation

To use this node in KNIME, install Cresset KNIME Nodes from the following update site:

KNIME 4.3

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Developers

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