Epik Panel

In the Epik panel you can set up and run a job that predicts the pKa of the ionizable atoms in your structures, or generates structures with probable ionization and tautomerization states based on the predicted pKa values.

To open this panel: click the Tasks button and browse to Ligand Preparation and Library Design → ML Model pKa

  • Using
  • Features
  • Additional Resources

Using the Epik Panel

Epik version 7 (Epik) is a complete redesign of Introduction to Epik Classic—the classic pKa and protonation state prediction software—that leverages Schrödinger’s powerful machine learning platform for more accurate results across broader chemical space.

For information regarding Epik Background and types of calculations, see the Epik User Manual.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see epikx Command Help.

Epik Panel Features

 

Structure Source option menu

Choose the structure source for the calculations.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
  • 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 select or include the entries for the structure source.

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.

Generate states checkbox

The Generate states checkbox is unchecked by default if there are no structures in the workspace (it is checked by default if there are structures in the workspace). When unchecked, the pKa property will be added to the existing structures. If checked, you can adjust the protonation states. For information about the output of this calculation, see Epik Calculation Modes.

pH range text boxes

Specify the target pH value and the amount of variation from this value inside which the generated ionization states can have a significant population.

The default pH of 7.4 was chosen simply because it is the center of the scale, the value for a neutral aqueous solution. The pH in biological systems can deviate from this value, e.g. for normal blood it is 7.4, whereas it is lower in the extracellular environment for tumors.

The range is converted into a probability of 10−range. Ionized (and tautomerized) structures whose probability exceeds this value, when all likely structures are considered, are kept. If the structure does not tautomerize, this is equivalent to keeping structures whose groups are ionized if their pKa lies within the specified range of the target pH value.

Output - maximum # structures per molecule text box

Enter the maximum number of structures to be generated for each input structure in this text box. If the number of structures with significant probability in the given pH range is greater than this number, return the most probable structures.

Create speciation report option

Select to create an HTML file containing a pKa report for predicting states mode. This option is only available when there is a single structure specified as input. Upon the completion of a job, you can view the report by importing the output into the Project Table and selecting View Speciation Report from the Workflow Action Menu .

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Epik - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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