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
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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Binding site shape clustering consists of the following 53 nodes(s):
Binding site shape clustering contains nodes provided by the following 5 plugin(s):
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