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Maestro
Nodes Protein Scripting Library Design Phase PyMOL Visualization Canvas ConfGen
  1. Workflow
    Bioisoster enumeration
    Library Design Maestro
    Functional groups are replaced with bioisosteres that are available in the literature. [Requires: Maestro]
    schroedinger > Workflow_examples > Library design > Bioisoster replacement > Bioisoster replacement
    1
    schroedinger
  2. Workflow
    Run Maestro and Run Maestro command
    Nodes Maestro
    Automate some rendering preparation and inspect structures in Maestro. Select residues interactively in Maestro and use this sele…
    schroedinger > Workflow_examples > Visualization > Run Maestro > Run Maestro, command
    0
    schroedinger
  3. Workflow
    Split and align multimers
    Protein Maestro
    Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
    schroedinger > Workflow_examples > Protein > Split and align multimers > Split multimers 1-3
    0
    schroedinger
  4. Workflow
    Protein Structure Alignment
    Protein Maestro
    Extract one monomer from each of the two multimers. Align the binding sites (via the 'Align Binding Sites' node) or the whole str…
    schroedinger > Workflow_examples > Protein > Alignment > Protein Alignment
    0
    schroedinger
  5. Workflow
    Library enumeration
    Library Design Maestro
    Create libraries by substituting one or several attachments on a core structure with fragments from reagent compounds. Unique ide…
    schroedinger > Workflow_examples > Library design > Enumeration > R group enumeration
    0
    schroedinger
  6. Workflow
    Chemistry External Tool Node Use-cases
    Scripting Maestro Phase
    The Chemistry external tool nodes can be used to parse a log file with basic shell commands, run Shrodinger utilities or backends…
    schroedinger > Workflow_examples > Scripting > Chemistry external tool > Chemistry external tool 1
    0
    schroedinger
  7. Workflow
    Multiple Sequence Viewer
    Nodes Maestro
    Opens the Multiple Sequence Viewer panel to visualize sequences or edit an alignement. [Requires: Maestro]
    schroedinger > Workflow_examples > _Nodes > Multiple Sequence Viewer > Multiple Sequence Viewer
    0
    schroedinger
  8. Workflow
    Run PyMOL
    Maestro PyMOL Visualization
    Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: M…
    schroedinger > Workflow_examples > Visualization > Run PyMOL > Run PyMOL 1-2
    0
    schroedinger
  9. Workflow
    Chemistry External Tool Node Use-cases
    Scripting Maestro Phase
    +1
    The Chemistry external tool nodes can be used to parse a log file with basic shell commands, run Shrodinger utilities or backends…
    schroedinger > Workflow_examples > Scripting > Chemistry external tool > Chemistry external tool 1-2
    0
    schroedinger
  10. Workflow
    Run Maestro and Run Maestro command
    Nodes Maestro
    Automate some rendering preparation and inspect structures in Maestro. Select residues interactively in Maestro and use this sele…
    faesslja > Public > Run Maestro, command
    0
    faesslja
  11. Workflow
    Readers and Writers
    Nodes Maestro
    Read and write structure files. Read a list of PDB files from a directory. [Requires: Maestro] See also: - Docking - Grid generat…
    schroedinger > Workflow_examples > _Nodes > Readers and Writers > Readers and Writers
    0
    schroedinger
  12. Workflow
    Conformer cluster
    Nodes Maestro ConfGen
    Cluster conformers based on Cartesian or torsional RMSD. [Requires: Maestro, ConfGen]
    schroedinger > Workflow_examples > _Nodes > Conformer cluster > Conformer cluster
    0
    schroedinger
  13. Workflow
    Chemistry External Tool Node Use-cases
    Nodes Maestro
    The Chemistry external tool nodes can be used to parse a log file with basic shell commands or run any command line utilities. Qu…
    schroedinger > Workflow_examples > _Nodes > Chemistry external tool node > Chemistry external tool
    0
    schroedinger
  14. Workflow
    Semiempirical optimization
    Quantum Mechanics Maestro LigPrep
    Run semi-empirical NDDO quantum chemical optimization and generate surface properties [Requires: Maestro, LigPrep]
    schroedinger > Workflow_examples > Quantum Mechanics > Semiempirical NDDO > Semiempirical
    0
    schroedinger
  15. Workflow
    Split and align multimers
    Protein Maestro
    Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
    schroedinger > Workflow_examples > Protein > Split and align multimers > Split multimers 1-2
    0
    schroedinger
  16. Workflow
    Split and align multimers
    Protein Maestro
    Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
    schroedinger > Workflow_examples > Protein > Split and align multimers > Split multimers 1
    0
    schroedinger
  17. Workflow
    Run Maestro Command Node Use-cases
    Scripting Maestro Macromodel
    The Run maestro command node is used to alter the formal charge of some atoms defined by an ASL and for altering the structure re…
    schroedinger > Workflow_examples > Scripting > Maestro commands > Maestro commands
    0
    schroedinger
  18. Workflow
    Highlight residues
    Scripting Maestro
    HIghlight and label residues selected on a list. [Requires: Maestro]
    schroedinger > Workflow_examples > Scripting > Maestro commands > Maestro commands - highlight residues
    0
    schroedinger
  19. Workflow
    Ensure Molecule Title Uniqueness
    General Maestro Canvas
    Ensure unique molecule titles (using the KNIME RowID or the Schrödinger dedicated node). This is useful in the context of Canvas.…
    schroedinger > Workflow_examples > General > Unique molecule titles > Unique molecule titles
    0
    schroedinger
  20. Workflow
    Run PyMOL
    Maestro PyMOL Visualization
    Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: M…
    schroedinger > Workflow_examples > Visualization > Run PyMOL > Run PyMOL 1
    0
    schroedinger