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]

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