Creating a New Experiment

You can create a new experiment for a study that optimizes the model, transforms the input molecules, and scores and filters the molecules generated.

Before you begin: Create a project and study before you create an experiment. See Creating a Project and Creating a Study and Defining the Target Product Profile.
See Also
Using Parameters from a Previous Experiment
Creating an Experiment from an Existing Iteration
Creating and Running Experiments
  1. From the home page, click Projects, Studies, and Experiments.
  2. Open a study and click Create an Experiment.

    Note: You can also click the arrow for a study and choose New Experiment.

  3. Define the Title and optional Description for the experiment.

    The Title is prepopulated with a time and date stamp. You can add text to it or replace it as required.

  4. Click the Molecules tab and define input molecules.
    • Click to drag an SD file with the molecules from 3DDrive.
    • Click to open the Pipette Sketcher tool to draw molecules.
    • Click to paste in SMILES strings separated by semicolons.
    • Click to select all molecules.
    • Click to delete selected molecules.

    Notes:
    • Experiments that use a Reaction Enumeration or Rgroup Enumeration method do not require input molecules—the Molecule tab is not available if you choose one of those methods.
    • You can choose structures in the input atoms to retain in the generated molecules. For more information, see Defining Structures to Retain in an Input Molecule.
    • You can use Pipette Sketcher identify a location where changes are restricted to members of a homology group. All parts of the molecule other than the homology group remain stable. Homology groups can only be used in terminal locations (not as linkers). For more information, see Using Homology Groups in Input Molecules.

  5. Optional: If you specify design space molecules, an additional optimization criterion penalizes generated molecules that are not like the targets.
    • Select input molecules individually or click to select all, and then click Add selected as Design Space Molecules.
    • Click to drag an SD file with the molecules from 3DDrive.
    • Click to open the Pipette Sketcher tool to draw molecules.
    • Click to paste in SMILES strings separated by semicolons.
    • Click to delete selected molecules.
  6. Click the Parameters tab and define the parameters for the experiment.

    Parameters are available in four tabs:

    • Optimize: Parameters for optimization and controlling the length of the experiment.
      Note: Using a pharmacophore model requires the Generative Therapeutics Scientist or the Small Molecule Scientist role. If the Pharmacophore Model parameters are not available, contact your 3DS sales representative.
    • Generate: Parameters that affect molecule generation.
    • Filter: Parameters for methods of filtering generated molecules.
    • Score: Parameters for scoring molecules that pass the filter criteria.

    Tips:
    • Click for parameter help.
    • You can use the parameter values from a previous experiment. For more information, see Using Parameters from a Previous Experiment.
    • Values next to the parameter field are calculated automatically based on the input molecules. Click the value to populate the parameter field with it.
    • Click Load default parameters to load the default values for the parameters.
    • Click Show Advanced Parameters to show advanced settings. Click again to hide.
    • If you are using the Rgroup Enumeration or Reactant Enumeration generation methods, see Rgroup Enumeration and Reaction Enumeration for more information.

  7. Click Save or Run.

    • Changes are saved when you click Run.
    • Once you run an experiment, you cannot make changes and run it again.
    • If you saved the experiment previously, you can navigate back to it and make additional changes and either Save changes or Run when you are ready.
    • Each GTD user can run up to four concurrent experiments.
    • Click Stop to cancel a running experiment.

After the experiment completes:
  • Review convergence charts after running an experiment to verify the optimization of properties. For more information, see Viewing Convergence.
  • View the results in GTD. For more information, see Opening Results.
  • If an experiment ended with no results, the filters and parameters responsible are summarized in the Comments tab.
  • The data is available in the Insight for Research app for further visualization and analysis. For more information, see the Insight for Research User's Guide. Also, the top molecules generated are available to users of the Materials Registration app.