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Grid generation 1-3

Protein preparation and Glide grid generation

Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and display the ligand structures in 2D.

[Requires: Glide]

Protein preparation and Glide grid generation: Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition anddisplay the ligand structures in 2D.[Requires: Glide]Inspect the structures3 kinasesLigands in complexesWith their PDB name and numberTitle: PDB IDAutomatic ligand detectionPreparation in one step Names based on the PDB IDsGrid pathsGlide grid pathsin the GlideGrid columnGrid namesLigands docked in the Glide grid written on disk%file%Glide grid pathsin the table%file%Ligands to dock%file%Run Maestro Get PDB Table Viewer Ligand extraction Extract Properties Glide GridGeneration Protein PreparationWizard Align Binding Sites Glide Grid Reader Chunk Loop Start Loop End Glide Grid Writer ChemistryExternal Tool Table Viewer Table Creator Table Viewer Molecule Writer(from MAE) Table Viewer CSV Writer Molecule Reader(to MAE) Glide LigandDocking Grid Path Test in batch CSV Writer Protein preparation and Glide grid generation: Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition anddisplay the ligand structures in 2D.[Requires: Glide]Inspect the structures3 kinasesLigands in complexesWith their PDB name and numberTitle: PDB IDAutomatic ligand detectionPreparation in one step Names based on the PDB IDsGrid pathsGlide grid pathsin the GlideGrid columnGrid namesLigands docked in the Glide grid written on disk%file%Glide grid pathsin the table%file%Ligands to dock%file%Run Maestro Get PDB Table Viewer Ligand extraction Extract Properties Glide GridGeneration Protein PreparationWizard Align Binding Sites Glide Grid Reader Chunk Loop Start Loop End Glide Grid Writer ChemistryExternal Tool Table Viewer Table Creator Table Viewer Molecule Writer(from MAE) Table Viewer CSV Writer Molecule Reader(to MAE) Glide LigandDocking Grid Path Test in batch 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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On NodePit since: 2020-02-17
Last update: 2020-02-26
Created with KNIME version: v4.1.0
Tags: DockingGlide

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