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Docking
Glide
LigPrep Prime QikProp Binding Site Volume Canvas Clustering Molecular Dynamcis Real World
  1. Workflow
    Docking and Scoring
    Docking LigPrep Glide
    +1
    Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing wi…
    schroedinger > Workflow_examples > Docking > Docking > Docking 1-2
    1
    schroedinger
  2. Workflow
    Docking and Scoring
    Docking LigPrep Glide
    +1
    Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing wi…
    schroedinger > Workflow_examples > Docking > Docking > Docking 1
    0
    schroedinger
  3. Workflow
    Loop Over Docking Parameters
    Docking Glide
    Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [Requires: Glid…
    jackmarkham > Public > Loop over parameters
    0
    jackmarkham
  4. Workflow
    Core constraint
    Docking Glide LigPrep
    Compounds are docked with a core constraint using the MCS with the reference ligand.
    schroedinger > Workflow_examples > Docking > Core constraint > Core constraint
    0
    schroedinger
  5. Workflow
    Validate Docking Parameters
    Docking Glide LigPrep
    +1
    Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare…
    schroedinger > Workflow_examples > Docking > Validate parameters > Validate parameters 1-3
    0
    schroedinger
  6. Workflow
    Virtual Screening
    Docking Glide QikProp
    +1
    Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using dif…
    schroedinger > Workflow_examples > Docking > Virtual screening > Virtual screening 1-2
    0
    schroedinger
  7. Workflow
    Virtual Screening
    Docking Glide QikProp
    +1
    Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using dif…
    schroedinger > Workflow_examples > Docking > Virtual screening > Virtual screening 1-3
    0
    schroedinger
  8. Workflow
    Protein preparation and Glide grid generation
    Docking Glide
    Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand c…
    schroedinger > Workflow_examples > Docking > Grid generation > Grid generation 1
    0
    schroedinger
  9. Workflow
    Docking and Scoring
    Docking LigPrep Glide
    +1
    Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing wi…
    kshin > Public > Docking 1
    0
    kshin
  10. Workflow
    Docking and Scoring
    Docking LigPrep Glide
    +1
    Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing wi…
    schroedinger > Workflow_examples > Docking > Docking > Docking 1-3
    0
    schroedinger
  11. Workflow
    Protein preparation and Glide grid generation
    Docking Glide
    Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand c…
    schroedinger > Workflow_examples > Docking > Grid generation > Grid generation 1-2
    0
    schroedinger
  12. Workflow
    Protein preparation and Glide grid generation
    Docking Glide
    Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand c…
    schroedinger > Public > Recent_requests > Grid generation with H-bond constraints
    0
    schroedinger
  13. Workflow
    Virtual Screening
    Docking Glide QikProp
    +1
    Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using dif…
    schroedinger > Workflow_examples > Docking > Virtual screening > Virtual screening 1
    0
    schroedinger
  14. 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
  15. Workflow
    Protein preparation and Glide grid generation
    Docking Glide
    Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand c…
    schroedinger > Workflow_examples > Docking > Grid generation > Grid generation 1-3
    0
    schroedinger
  16. Workflow
    Validate Docking Parameters
    Docking Glide LigPrep
    +1
    Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare…
    schroedinger > Workflow_examples > Docking > Validate parameters > Validate parameters 1
    0
    schroedinger
  17. Workflow
    Loop Over Docking Parameters
    Docking Glide
    Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [Requires: Glid…
    schroedinger > Workflow_examples > Docking > Loop over parameters > Loop over parameters
    0
    schroedinger
  18. Workflow
    Validate Docking Parameters
    Docking Glide LigPrep
    +1
    Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare…
    schroedinger > Workflow_examples > Docking > Validate parameters > Validate parameters 1-2
    0
    schroedinger
  19. Workflow
    Ensemble Docking
    Docking Glide
    Dock ligands into multiple conformations of the binding site and report the best pose per ligand. [Requires: Glide]
    schroedinger > Workflow_examples > Docking > Ensemble docking > Ensemble docking
    0
    schroedinger