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Docking
Glide LigPrep Prime 4-Dimensional Quantitative Structure-Activity Relationship 4D-QSAR CADD Cheminformatics Computer-Aided Drug Design Drug Design LigandScout
  1. Workflow
    Evotec_StructureBasedVirtualScreening_Calibration
    Decoy Sbvs Calibration
    +6
    Workflow for Structure-based Virtual Screening calibration There are two main parts 1) decoy generation 2) docking evaluation usi…
    emilie_pihan > Evotec > Evotec_StructureBasedVirtualScreening_Calibration
    2
    emilie_pihan
  2. Workflow
    Assessment of Vina for SARS-CoV-2 Main Protease
    Drug Discovery Drug Design Cheminformatics
    +5
    There has been no description set for this workflow's metadata.
    arashsadri > Biological Sciences and Physics Unified Internal Evolution and Urging the Second Scientific Revolution > Assessment of Vina for SARS-CoV-2 Main Protease
    2
    arashsadri
  3. Node / Manipulator
    AutoDock 4
    LigandScout Docking
    The AutoDock 4 node enables docking experiments via AutoDock 4.
    1
    inteligand
  4. Node / Manipulator
    AutoDock Vina
    LigandScout Docking
    The AutoDock Vina node enables docking experiments via AutoDock Vina.
    1
    inteligand
  5. 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
  6. Workflow
    4D-QSAR Docking of ChEMBL Ligands
    Docking Binding Affinity 4D-QSAR
    +6
    There has been no description set for this workflow's metadata.
    arashsadri > Biological Sciences and Physics Unified Internal Evolution and Urging the Second Scientific Revolution > 4D-QSAR Docking of ChEMBL Ligands
    1
    arashsadri
  7. Workflow
    4D-QSAR ML Only Binding Features
    Drug Discovery Drug Design Cheminformatics
    +5
    There has been no description set for this workflow's metadata.
    arashsadri > Biological Sciences and Physics Unified Internal Evolution and Urging the Second Scientific Revolution > 4D-QSAR ML Only Binding Features
    1
    arashsadri
  8. Workflow
    4D-QSAR Docking Selected COVID-19 Drugs
    Drug Discovery Drug Design 4-Dimensional Quantitative Structure-Activity Relationship
    +6
    There has been no description set for this workflow's metadata.
    arashsadri > Biological Sciences and Physics Unified Internal Evolution and Urging the Second Scientific Revolution > 4D-QSAR Docking Selected COVID-19 Drugs
    1
    arashsadri
  9. Workflow
    PIPER with constraints
    Schrodinger Docking PIPER
    Runs PIPER docking to generate protein-protein complexes using constraints.
    schroedinger > Workflow_examples > Docking > PIPER > PIPER with constraints
    0
    schroedinger
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  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
    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
  18. 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
  19. 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
  20. 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