Predictive Tox SAR Panel (Beta)
Run structure-activity relationship analysis using predictive toxicology models to evaluate ligand binding affinity predictions.
To display this panel- click the Tasks button and browse to Induced Fit Docking → Predictive Tox SAR (Beta)
- Using
- Features
- Additional Resources
Predictive Tox SAR Panel (Beta) Features
- Setup tab
- Use structures from option menu
Choose the structure source for the current task.
- Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
- File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
- Open Project Table button
Open the Project Table panel, so you can
- File name text box and Browse button
Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.
- Ligands table
Displays the loaded ligands. The table includes the ligand name, health status, a Sided Error column, and the affinity score from the property selected in Experimental affinity. The score column header shows the selected affinity units.
In the Sided Error column, set a compound to = when its affinity value is an exact measurement, or to > or < when the value is an off-assay measurement that represents an assay detection limit rather than a precise value. The affinity score for a compound marked > or < is shown in gray to indicate that it is a detection limit.
- Delete button (
) Click this button to remove the selected ligands from the table.
- Target option menu
Choose the protein target for binding prediction. Click to open a searchable list of targets, each shown with its family in parentheses. Type in the search box to filter the list by target or family name.
- Experimental affinity setting
Click Define to open a popup in which you select the structure-level property that contains the experimental affinity values for the ligands, and choose the units from the Units option menu. Only properties with numeric values that are common to all loaded ligands are listed. The selected property values are displayed in the ligands table.
- 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.
- 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.
- Analysis tab
- Load results from text box
Specify the directory that contains the results from a completed job.
- Results table
Displays the results for each model, including R-squared and RMSE scores. The scores are color-coded to indicate model quality.
- Graph area
Displays the graph for the selected result in the table.
- Download .fmp file button
Export the selected result as an FMP file to a chosen location.
- View in FEP+ button
Open the selected result in the FEP+ panel.