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Sitemap and docking

Sitemap and Glide Grid Generation

Prepare a set of PDB structures and identify possible binding sites with Sitemap.
Generate receptor grids with Glide for each site and used to dock ligands

[Requires: SiteMap, Glide] [Keywords: binding site, ensemble docking, grid generation, druggability]

Sitemap and Glide Grid Generation:Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock ligands[Requires: SiteMap, Glide] [Keywords: binding site, ensemble docking, grid generation, druggability]DisabledCompare the binding sitesScores < -5 Ensemble docking Protein-ligand complexesProtein and largest ligandSite visualizationSite propertiesBest binding sitefor each ligand Surface lastFind the possible binding sitesAround the centroid of the sitesDscore SiteMap To be used outside of KNIMELigands to dockTesting Table Viewer Number ofgood scores Glide LigandDocking Chunk Loop Start Loop End Get PDB Protein PreparationWizard Split complexes Run Maestro Table Viewer Table Viewer Best binding site Column Resorter SiteMap Grid generation Most druggable Extract Properties Glide Grid Writer Molecule Reader(to MAE) Group MAE Sitemap and Glide Grid Generation:Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock ligands[Requires: SiteMap, Glide] [Keywords: binding site, ensemble docking, grid generation, druggability]DisabledCompare the binding sitesScores < -5 Ensemble docking Protein-ligand complexesProtein and largest ligandSite visualizationSite propertiesBest binding sitefor each ligand Surface lastFind the possible binding sitesAround the centroid of the sitesDscore SiteMap To be used outside of KNIMELigands to dockTesting Table Viewer Number ofgood scores Glide LigandDocking Chunk Loop Start Loop End Get PDB Protein PreparationWizard Split complexes Run Maestro Table Viewer Table Viewer Best binding site Column Resorter SiteMap Grid generation Most druggable Extract Properties Glide Grid Writer Molecule Reader(to MAE) Group MAE

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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: 2023-12-14
Last update: 2024-12-17
Created with KNIME version: v4.1.3
Tags: Real WorldSiteMapGlideBinding SiteEnsemble DockingGrid GenerationDruggability

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