A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime and the RMSDs are reported to assess the pose stability. The workflow can be used to refine for instance on a docking based alignment to prepare the input of a FEP calculation.
Workflow
Ligand alignment MD refinement
Used extensions & nodes
Created with KNIME Analytics Platform version 4.1.0 Note: Not all extensions may be displayed.
- Go to item
KNIME AG, Zurich, Switzerland
Version 4.1.0
- Go to item
KNIME AG, Zurich, Switzerland
Version 3.7.0
- Go to item
Schrödinger
Versions 19.4.6, 20.1.11
Legal
By using or downloading the workflow, you agree to our terms and conditions.