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Schrodinger
LigPrep
LiveDesign
Glide MacroModel QikProp Shape screening Epik Phase pharmacophore SiteMap
  1. Workflow
    Torsion_profiles
    Schrodinger MacroModel LigPrep
    +1
    Performes a torsion scan for a defined dihedral using MacroModel and returns the energy profile. 22.2.4
    schroedinger > LiveDesign_models > Plotting > Torsion profiles
    0
    schroedinger
  2. Workflow
    Highlight substructure
    LiveDesign QikProp LigPrep
    +1
    Highlight the substructure in the input structures. Only the substructure query is reported if it isn't found. [21.4.1]
    schroedinger > LiveDesign_models > Structure operation > Highlight substructure
    0
    schroedinger
  3. Workflow
    MM partial charges
    LiveDesign LigPrep Schrodinger
    Returns 3D structure of molecule with labels of partial charges on heavy atoms and polar hydrogen. Force field (OPLS) charges are…
    schroedinger > Internal development > 22-3 > atom_charge_labels > MM charges --- 0530 JK
    0
    schroedinger
  4. Workflow
    Ensemble docking
    LiveDesign Glide LigPrep
    +1
    Docks the compounds with Glide in 2 binding site conformations and reports the binding site conformation where it scores the best…
    schroedinger > Internal development > 22-4 > validated_models > Docking > Ensemble docking
    0
    schroedinger
  5. Workflow
    MM partial charges
    LiveDesign LigPrep Schrodinger
    Returns 3D structure of molecule with labels of partial charges on heavy atoms and polar hydrogen. Force field (OPLS) charges are…
    schroedinger > Internal development > 22-3 > DeepAutoQSAR > MM charges --- 0530 JK
    0
    schroedinger
  6. Workflow
    NDDO partial charges
    LiveDesign LigPrep Schrodinger
    Returns 3D structure of molecule with labels of partial charges on heavy atoms and polar hydrogen. Semiempirical (NDDO) charges a…
    schroedinger > Internal development > 22-3 > DeepAutoQSAR > NDDO charges --- 0530 JK
    0
    schroedinger
  7. Workflow
    Docking and ligand strain
    LiveDesign Glide LigPrep
    +2
    Docks the compounds with Glide. The docking pose are minimized to a local minimum and a conformational search is run to find the …
    schroedinger > Internal development > 23-1 > Docking with core constraint
    0
    schroedinger
  8. Workflow
    Docking and rendering
    LiveDesign Glide LigPrep
    +1
    Docks the compounds with Glide and changes the rendering of the binding site (atoms displayed, residues labelled and the atom rep…
    schroedinger > Internal development > 22-4 > validated_models > Docking > Docking and rendering
    0
    schroedinger
  9. Workflow
    Ligand CNS desirability radar plot
    LiveDesign LigPrep Schrodinger
    Generates radar plots for the CNS desirability MPO properties. 21.2.0
    schroedinger > LiveDesign_models > Plotting > Ligand CNS desirability plot
    0
    schroedinger
  10. Workflow
    Ligand CNS desirability range plot
    LiveDesign LigPrep Schrodinger
    Generates radar plots of the CNS desirability MPO properties calculated on the LiveReport compound structures and the number of r…
    schroedinger > LiveDesign_models > Plotting > Ligand CNS desirability range plot
    0
    schroedinger
  11. Workflow
    Torsion_profiles
    Schrodinger MacroModel LigPrep
    +1
    Performes a torsion scan for a defined dihedral using MacroModel and returns the energy profile. 22.2.4
    schroedinger > Internal development > 22-4 > validated_models > Plotting > Torsion_profiles
    0
    schroedinger
  12. Workflow
    Docking and rendering
    LiveDesign Glide LigPrep
    +1
    Docks the compounds with Glide and changes the rendering of the binding site (atoms displayed, residues labelled and the atom rep…
    schroedinger > LiveDesign_models > Docking > Docking and rendering
    0
    schroedinger
  13. Workflow
    Docking and ligand strain
    LiveDesign Glide LigPrep
    +2
    Docks the compounds with Glide. The docking pose are minimized to a local minimum and a conformational search is run to find the …
    schroedinger > Internal development > 22-4 > validated_models > Docking > Docking and ligand strain
    0
    schroedinger
  14. Workflow
    Ligand alignment by shape with a flexible reference
    LiveDesign Shape screening LigPrep
    +1
    Aligns ligands on a reference structure treated flexibly as well, using Shape screening. [32102] 22.2.4
    schroedinger > Internal development > 22-4 > validated_models > Structure alignment > Ligand alignment by shape with a flexible reference
    0
    schroedinger
  15. Workflow
    Ligand alignment with a cocrystallized reference
    LiveDesign LigPrep Schrodinger
    It aligns the structures on a reference ligand kept rigid using align_ligands utility. [32358] 22.2.4
    schroedinger > LiveDesign_models > Structure alignment > Ligand alignment with a cocrystallized reference
    0
    schroedinger
  16. Workflow
    Ligand alignment by shape with a flexible reference
    LiveDesign Shape screening LigPrep
    +1
    Aligns ligands on a reference structure treated flexibly as well, using Shape screening. [32102] 22.2.4
    schroedinger > LiveDesign_models > Structure alignment > Ligand alignment by shape with a flexible reference
    0
    schroedinger
  17. Workflow
    Docking and ligand strain
    LiveDesign Glide LigPrep
    +2
    Docks the compounds with Glide. The docking pose are minimized to a local minimum and a conformational search is run to find the …
    schroedinger > LiveDesign_models > Docking > Docking and ligand strain
    0
    schroedinger
  18. 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
  19. Workflow
    QSAR - Random forest
    LiveDesign LigPrep QikProp
    +1
    Reports the predictions of a pregenerated random forest QSAR model run on physicochemical properties generated with QikProp from …
    schroedinger > LiveDesign_models > Cheminformatics > QSAR - random forest
    0
    schroedinger
  20. Workflow
    NDDO charges
    LiveDesign LigPrep Schrodinger
    Returns 3D structure with labels of partial charges on heavy atoms and polar hydrogen. Semiempirical (NDDO) charges are applied. …
    schroedinger > Internal development > 22-3 > atom_charge_labels > NDDO charges --- 0525 JK
    0
    schroedinger