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SiteMap
Glide Schrodinger LiveDesign Real World Binding Site Grid Generation Docking Homology Modeling LigPrep
  1. Workflow
    Sitemap and Glide Grid Generation
    Real World SiteMap Glide
    +4
    Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each sit…
    schroedinger > Workflow_examples > Real world > Sitemap and docking > Sitemap and docking
    0
    schroedinger
  2. Workflow
    Docking and protein surface
    LiveDesign Glide LigPrep
    +2
    Docks the compounds with Glide. Also generates the protein surface and changes the rendering of the binding site (atoms displayed…
    schroedinger > Workflow_examples > LiveDesign > Docking > Docking and protein surface
    0
    schroedinger
  3. Workflow
    Binding site shape clustering
    Real World SiteMap Canvas
    +5
    Analyze a set of PDB structures (or a molecular dynamics trajectory) with SiteMap to characterize frames for possible binding sit…
    schroedinger > Workflow_examples > Real world > Binding site shape clustering > Binding site shape clustering
    0
    schroedinger
  4. Workflow
    Protein model building on an edited alignment
    Real World Prime Glide
    +6
    Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and …
    schroedinger > Workflow_examples > Protein > Model building on a template > Model building on a template 1
    0
    schroedinger
  5. Workflow
    Protein model building on an edited alignment
    Real World Prime Glide
    +6
    Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and …
    schroedinger > Workflow_examples > Protein > Model building on a template > Model building on a template 1-2
    0
    schroedinger
  6. Workflow
    SiteMap binding site characterization
    Docking SiteMap
    Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: …
    schroedinger > Workflow_examples > Docking > Binding site > Binding site 1-3
    0
    schroedinger
  7. Workflow
    Docking and protein surface
    LiveDesign Glide LigPrep
    +2
    Docks the compounds with Glide. Also generates the protein surface and changes the rendering of the binding site (atoms displayed…
    schroedinger > LiveDesign_models > Docking > Docking and protein surface
    0
    schroedinger
  8. Workflow
    Interaction surface
    LiveDesign Schrodinger Sitemap
    Adds the binding pocket interaction surface generated with SiteMap. [32391] 21.3.0 See details in https://kni.me/w/RTAj4YehKE4nNe…
    schroedinger > Workflow_examples > LiveDesign > Docking post-processing > Interaction surface
    0
    schroedinger
  9. Workflow
    Interaction surface
    LiveDesign Schrodinger Sitemap
    Adds the binding pocket interaction surface generated with SiteMap. [32391] 21.3.0 See details in https://kni.me/w/RTAj4YehKE4nNe…
    schroedinger > LiveDesign_models > Docking post-processing > Interaction surface
    0
    schroedinger