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Ligand alignment MD refinement 1

Ligand alignment MD refinement

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.

Ligand alignment MD refinementA Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representativeframes are refined with Prime and the RMSDs are reported to assess the pose stability. The workflow can be used to refine forinstance on a docking based alignment to prepare the input of a FEP calculation. Matrix file nameLigand file nameon a custom msjon GPUAsynchronousLigandsWith ligands of the representative frames Representative frames Aligned to reference List all complexesand residue renaminginto UNKPose viewer fileGPUand CPUIn the workingdirectoryMoveand deleteAlignedIn the working directory readingon CPURMSD %file% RMSD matrices %file% String Manipulation(Variable) String Manipulation(Variable) Run Desmond Group Loop Start RMSD Get representative Align Binding Sites Alignment Column Filter Processing Loop End (2 ports) Job Control Protein-ligand Input Hosts CSV Writer Desmond TrajectoryManipulation Molecule Writer(from MAE) Trajectory Refine protein-ligandcomplexes CSV Writer CSV Writer Ligand alignment MD refinementA Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representativeframes are refined with Prime and the RMSDs are reported to assess the pose stability. The workflow can be used to refine forinstance on a docking based alignment to prepare the input of a FEP calculation. Matrix file nameLigand file nameon a custom msjon GPUAsynchronousLigandsWith ligands of the representative frames Representative frames Aligned to reference List all complexesand residue renaminginto UNKPose viewer fileGPUand CPUIn the workingdirectoryMoveand deleteAlignedIn the working directory readingon CPURMSD %file% RMSD matrices %file% String Manipulation(Variable) String Manipulation(Variable) Run Desmond Group Loop Start RMSD Get representative Align Binding Sites Alignment Column Filter Processing Loop End (2 ports) Job Control Protein-ligand Input Hosts CSV Writer Desmond TrajectoryManipulation Molecule Writer(from MAE) Trajectory Refine protein-ligandcomplexes CSV Writer CSV Writer

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: kphimister
Created at: 2018-06-06
On NodePit since: 2020-08-12
Last update: 2026-01-17
Created with KNIME version: v4.1.0
Tags: Molecular Dynamics

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