Epik Classic Panel

In the Epik Classic 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 → Empirical pKa .

A panel titled pKa and Protonation State Predictions opens. Click the Epik-Classic button.

 

  • Using
  • Features
  • Additional Resources

Using the Epik Classic Panel

The tasks available from the Epik Classic panel are the prediction of the pKa values of the ionizable atoms in a set of structures, either for independent or for successive protonation or deprotonation, and the generation of the probable ionized (and tautomerized) states of a set of structures within a given pH range. The pKa predictions are rule-based, and so can be generated very rapidly. The pKa values are stored as atom-level properties with the structure.

When the Epik Classic job finishes, the pKa values are automatically displayed on the structures in the Workspace as atom labels. The labels can be cleared from the Style toolbox. Uncertainties are provided with the pKa predictions.

Epik Classic produces a number of properties that are listed in the Project Table. The most important of these are:

  • State Penalty—The free energy of this state in the ensemble of states generated, in kcal/mol (smaller is better).
  • Metal State Penalty—Similar to the State Penalty except this is used when key deprotonated, ligand atoms lie close to a metal in a metalloprotein.
  • Tot Q—The total charge on this state.
  • tautomer probability—The fraction of the population of the states at the same charge level that this state represents.

To predict independent pKa values for a set of structures:

  1. Select the source of the structures using the tools at the top of the panel.

  2. Select the Query only option for the Analysis mode.

  3. Choose the solvent from the Solvent option menu.

  4. Click Run.

To generate the ionization and tautomerization states of structures within a given pH range:

  1. Select the source of the structures using the tools at the top of the panel.

  2. Select the Predict states option for the Analysis mode.

  3. Choose the solvent from the Solvent option menu.

  4. Enter the target pH and range in the pH text boxes.

  5. If you want to keep the original ionization state, regardless of its probability in the given pH range, select Include original ionization state.

  6. If the structures tautomerize, either in the original or the ionized state, select Generate tautomers. To keep the original tautomer, regardless of its probability in the given pH range, select Include original tautomer.

  7. If you are interested in structures bound to a metal in a protein, select Add metal-binding states.

  8. Enter the maximum number of structures to generate for each input structure in the Maximum number of output structures text box.

  9. Click Run.

To predict sequential pKa values for a set of structures:

  1. Select the source of the structures using the tools at the top of the panel.

  2. Select the Sequential pKa option for the Analysis mode.

  3. Choose the solvent from the Solvent option menu.

    This value is used to generate the most probable structure at the target pH as a reference for the pKa calculations. The range text box is not available.

  4. Select Generate tautomers to tautomerize structures during structural adjustment.

  5. Click Run.

If you have a large number of structures, you might want to make job settings to select a host and distribute the job over multiple processors before starting the job. To do so, choose Job Settings from the Settings button menu

and make the settings in the Job Settings dialog box. Then click Run to run the job.

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 epik Command Help.

Epik Classic Panel Features

Use structures from 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.

Analysis mode options

Query only: Predict pKa values of the input structures without doing any structural variation.

Predict states: Generate most probable states within a supplied pH range, and return structures as well as pKa values.

Sequential pKa values: Predict pKa values for successive protonation or deprotonation of the molecule. The pKa values are adjusted after the addition or removal of each proton.

Solvent option menu

Choose the solvent for the pKa predictions. The pKa values are stored for each solvent. The choices are H2O and DMSO.

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 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.

Include original ionization state option

When generating ionized output structures, keep the original ionization state, regardless of its relative probability in the given pH range.

pKa parameter file text box and Browse button

Enter the file name of a custom pKa parameter file, or click Browse and navigate to the file. See Epik Classic pKa Data File Format for more information.

Tautomer options

Generate tautomers option: If selected, generate tautomers of the original and ionized structure.

Include original tautomer option: If Generate tautomers is selected, this option ensures the inclusion of the original tautomeric state, regardless of its relative probability in the given pH range.

Tautomer parameter file text box and Browse button

Enter the file name of a custom tautomer parameter file, or click Browse and navigate to the file. See Epik Classic Tautomer Database Format for more information.

Add metal-binding states option

Generate states appropriate for binding to metals in a protein, in addition to those for solution. With this option selected, Epik Classic explores the removal of additional protons from heavy atoms that could potentially bind to metal atoms in the binding site of a protein.

Metal binding parameter file text box and Browse button

Enter the file name of a custom metal binding parameter file, or click Browse and navigate to the file.

Maximum number of output structures 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.

Job toolbar

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

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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