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Binding site shape clustering

Analyze a set of PDB structures (or a molecular dynamics trajectory) with SiteMap to characterize frames for possible binding sites.
Performed volume clustering on each Sitemap result to produce an ensemble of binding sites.
Generate receptor grids for ensemble docking with Glide

Based on:
Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols. Osguthorpe, D. J.; Sherman, W; Hagler, A. T. J. Phys. Chem. B 2012, 116, 6952−6959
Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering. Osguthorpe, D. J.; Sherman, W; Hagler, A. T. Chem Biol Drug Des 2012; 80: 182–193

[Requires: SiteMap, Canvas, Glide] [Keywords: binding site volume, clustering, docking, molecular Dynamics]

Binding site shape clustering:Analyze a set of PDB structures (or a molecular dynamics trajectory) with SiteMap to characterize frames for possible binding sites.Performed volume clustering on each Sitemap result to produce an ensemble of binding sites. Generate receptor grids for ensemble docking with GlideBased on: Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols. Osguthorpe, D. J.; Sherman, W; Hagler, A. T. J. Phys. Chem. B 2012, 116,6952−6959Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering. Osguthorpe, D. J.; Sherman, W; Hagler, A. T. Chem Biol Drug Des 2012; 80: 182–193[Requires: SiteMap, Canvas, Glide] [Keywords: binding site volume, clustering, docking, molecular Dynamics]DisabledProtein and largest ligand10 CDK2 complexesKeep only1 monomer.Unique titles Delete waters If the first structure has a ligand,skip otherwiseprepared sucessfully A single binding site region[configurable]Proteins and ligandsGrid generationAround the centroid of the sitesSitemap termsVolume clustering[configurable]Single binding siteSelected binding sites and corresponding ligandsInspect the selected binding sitesInspection preparation To be used outside of KNIMETesting Split complexes Get PDB Protein PreparationWizard Align Binding Sites Row Splitter Extract Properties SiteMap Table Viewer Run Maestro Glide Grid Writer Binding site shape clustering:Analyze a set of PDB structures (or a molecular dynamics trajectory) with SiteMap to characterize frames for possible binding sites.Performed volume clustering on each Sitemap result to produce an ensemble of binding sites. Generate receptor grids for ensemble docking with GlideBased on: Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols. Osguthorpe, D. J.; Sherman, W; Hagler, A. T. J. Phys. Chem. B 2012, 116,6952−6959Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering. Osguthorpe, D. J.; Sherman, W; Hagler, A. T. Chem Biol Drug Des 2012; 80: 182–193[Requires: SiteMap, Canvas, Glide] [Keywords: binding site volume, clustering, docking, molecular Dynamics]DisabledProtein and largest ligand10 CDK2 complexesKeep only1 monomer.Unique titles Delete waters If the first structure has a ligand,skip otherwiseprepared sucessfullyA single binding site region[configurable]Proteins and ligandsGrid generationAround the centroid of the sitesSitemap termsVolume clustering[configurable]Single binding siteSelected binding sites and corresponding ligandsInspect the selected binding sitesInspection preparation To be used outside of KNIMETesting Split complexes Get PDB Protein PreparationWizard Align Binding Sites Row Splitter Extract Properties SiteMap Table Viewer Run Maestro Glide Grid Writer

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On NodePit since: 2023-12-14
Last update: 2026-01-13
Created with KNIME version: v4.3.2
Tags: Real WorldSiteMapCanvasGlideBinding Site VolumeClusteringDockingMolecular Dynamcis

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