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Molecular Dynamics
Atom Selection Desmond Distance Hydrogen Bond Jobcontrol
+4
  1. Workflow
    Desmond simulation
    Molecular Dynamics Desmond Trajectory
    +5
    Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond net…
    schroedinger > Workflow_examples > Molecular Dynamics > MD simulation > MD simulation 1-2
    0
  2. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Workflow_examples > Molecular Dynamics > Ligand alignment MD refinement > Ligand alignment MD refinement 1
    0
  3. Workflow
    Metadynamics Analysis of Binding Poses
    Molecular Dynamics
    Various binding configurations of a single ligand in a single binding site are ranked.
    schroedinger > Workflow_examples > Molecular Dynamics > Binding Pose Metadynamics > Binding Pose Metadynamics
    0
  4. Workflow
    Desmond simulation
    Molecular Dynamics Desmond Trajectory
    +5
    Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond net…
    schroedinger > Workflow_examples > Molecular Dynamics > MD simulation > MD simulation 1
    0
  5. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Workflow_examples > Molecular Dynamics > Ligand alignment MD refinement > Ligand alignment MD refinement 1-2
    0
  6. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Internal development > 22-3 > Docking pose MD refinement > Docking pose MD refinement and event analysis --- DEVEL
    0
  7. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Internal development > 22-3 > Docking pose MD refinement > Docking pose MD refinement BKP
    0
  8. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Internal development > 22-3 > Docking pose MD refinement > Docking pose MD refinement and event analysis --- host control BKP 1
    0
  9. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Internal development > 22-3 > Docking pose MD refinement > Docking pose MD refinement and event analysis --- bolt
    0
  10. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Internal development > 22-3 > Docking pose MD refinement > Docking pose MD refinement and event analysis --- host control BKP
    0
  11. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Internal development > 22-3 > Docking pose MD refinement > Docking pose MD refinement and event analysis
    0
  12. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Internal development > 22-3 > Docking pose MD refinement > Docking pose MD refinement and event analysis --- before adapting to LD input
    0
  13. Workflow
    Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative fra…
    schroedinger > Internal development > 22-3 > Docking pose MD refinement > Docking pose MD refinement and event analysis --- host control
    0
  14. Node / Manipulator
    AMBER Trajectory Reader
    LigandScout Molecular Dynamics
    The AMBER Trajectory Reader node loads an AMBER MDCRD or NetCdf Trajectory file.
    0
  15. Node / Manipulator
    CHA Filter
    LigandScout Molecular Dynamics
    The CHA Filter node processes a list of pharmacophore models to only keep the unique ones. This filtering is based on the feature…
    0
  16. Node / Manipulator
    CHA Re-Score
    LigandScout Molecular Dynamics
    The CHA Re-Score node reads hit-lists (usually from the activity profiling node) and re-scores them according to their activity p…
    0
  17. Node / Manipulator
    DCD Trajectory Reader
    LigandScout Molecular Dynamics
    The DCD Trajectory Reader loads a CHARMM DCD trajectory file.
    0
  18. Node / Manipulator
    Desmond Molecular Dynamics
    Schrödinger Molecular Dynamics
    Molecular dynamics jobs simulate the Newtonian dynamics of the model system, producing a trajectory of the particles, coordinates…
    0
  19. Node / Manipulator
    Desmond System Builder
    Schrödinger Molecular Dynamics
    The System Builder panel allows you to set up a biological system consisting of proteins, ligands, explicit solvent, membrane, an…
    0
  20. Node / Manipulator
    Desmond Trajectory Extract Frames
    Schrödinger Molecular Dynamics
    Extracts selected frames from a Desmond trajectory into a table of output structures. Backend implementation trj2mae.py for Maest…
    0