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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]Compare the binding sitesNumber of good scores[configurable]Scores < -5 Ensemble docking Protein-ligand complexesSplit complexesProtein and largest ligandSite visualizationSite propertiesBest binding sitefor each ligandBest binding siteSurface lastFind the possible binding sitesGrid generationAround the centroid of the sitesOnly the most druggable[configurable]Dscore SiteMapText file To be used outside of KNIMELigands to dockTable Viewer Glide LigandDocking Chunk Loop Start Loop End Get PDB Protein PreparationWizard Run Maestro Table Viewer Table Viewer Column Resorter SiteMap Extract Properties CSV Writer 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]Compare the binding sitesNumber of good scores[configurable]Scores < -5 Ensemble docking Protein-ligand complexesSplit complexesProtein and largest ligandSite visualizationSite propertiesBest binding sitefor each ligandBest binding siteSurface lastFind the possible binding sitesGrid generationAround the centroid of the sitesOnly the most druggable[configurable]Dscore SiteMapText file To be used outside of KNIMELigands to dockTable Viewer Glide LigandDocking Chunk Loop Start Loop End Get PDB Protein PreparationWizard Run Maestro Table Viewer Table Viewer Column Resorter SiteMap Extract Properties CSV Writer 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: 2020-02-17
Last update: 2020-02-26
Created with KNIME version: v4.1.0
Tags: Real WorldSiteMapGlideBinding SiteEnsemble DockingGrid GenerationDruggability

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