Predictive Toxicology Panel
Screen a ligand for binding against a panel of protein toxicology targets to predict potential off-target binding.
To display this panel- click the Tasks button and browse to Induced Fit Docking → Predictive Tox
- Using
- Features
- Additional Resources
Predictive Toxicology Panel Features
- Setup tab
- Analysis tab
- Setup tab
Configure the input ligand, force field, and target selection for a predictive toxicology screening run.
- Input ligand from option menu
Select the source for the input ligand. Choose Project Table, Workspace, or File and click Load or Browse to load the ligand structure. The entry name is displayed below the option menu.
- Force field option menu
Choose the force field for the current task.
- Use customized version option
Use your customized version of the OPLS4 force field, rather than the standard version in the distribution.
If the customized version is missing or invalid, the text of this option turns orange and an orange warning icon is displayed to the right, with a tooltip about the problem.
- Parameter set button
Select the set of custom parameters for the OPLS4 force field. Opens the Set Custom Parameters Location Dialog Box.
- Select targets section
Select the protein targets for the screening run. The number of available targets is displayed in parentheses next to the label.
- Search targets text box
Enter text in this box to filter the target tree to the targets and families whose names match the text. Clear the box to show all targets again.
- Target tree
Hierarchical tree of the available protein targets, organized by family and, where a family has more than one sub-family, by sub-family. Select or clear the checkbox next to a target to include or exclude it from the screening run. Selecting or clearing the checkbox for a family or sub-family selects or clears all of the targets it contains, and a family or sub-family whose targets are only partly selected shows a mixed-state checkbox.
- Select All link
Click this link to select all targets currently shown in the tree.
- Deselect All link
Click this link to clear all targets currently shown in the tree.
- Job name text box and Host option menu
Specify a name for the job and choose a Job Server as a Service (JSS)-enabled host to run the job on. When you submit the job, a confirmation dialog box reports the estimated number of credits needed and the number of credits currently available. Writing the job files does not use credits. Credits are used only when the job runs.
- Contribute FEP data to improve future calculations of our ML model option
Select this option to permit Schrödinger to add the FEP output from this run to the training data for a machine learning model. The model is used to help guide and prioritize future calculations for all users, improving the efficiency and accuracy of the tools.
- Analysis tab
View and analyze the results of a completed predictive toxicology screening run.
- Load results from text box
Specify the path to the results directory. Click Browse to navigate to the directory.
- Ligand ID label
Displays the identifier of the ligand from the loaded results.
- Target table
Displays the targets and their predicted binding scores. Scores are color-coded to indicate binding affinity predictions. Selected targets are added to the Workspace and Entry List in a locked group.
- Overall score label
Displays the overall score for the selected target.
- Filter targets option menu
Choose a target family to show only the results for that family in the target table and the radar plot. Choose All to show every target.
- Radar plot
Displays a radar plot of scores across all targets when no target is selected in the table. When a target is selected, the radar plot is replaced by a ligand interaction diagram for the selected target.
- View Radar Plot link
Click this link to switch the display back to the radar plot view when a ligand interaction diagram is shown.