Amphiphilic Moment Panel

Calculate the amphiphilic moment of a set of molecules, which must be positively charged.

To open this panel: click the Tasks button and browse to ADME and Molecular Properties → Amphiphilic Moment.

  • Using
  • Features
  • Additional Resources

Using the Amphiphilic Moment Panel

This panel allows you to calculate the amphiphilic moment of a set of molecules that are positively charged. This property often correlates with certain ADME/Tox endpoints, such as phospholipidosis.

The algorithm involves calculation of ClogP values (octanol/water partition coefficient) for the atoms or groups in the structure and then produces a moment value by summing the product of the ClogP value for the atom and the vector from the positive center to the atom. A conformational search is performed on each structure, and the conformer with the highest amphiphilic moment is returned. If a structure has multiple positively-charged centers, the centroid of charges is used as the "positive center". See Fischer et al. J. Med. Chem. 2012, 55, 3227, for more information on the method.

If you want to run the calculations from the command line, use the following command:

$SCHRODINGER/structurebased_adme amphiphilic [options] structure-file

You can visualize the contributions to the amphiphilic moment in the Prime Energy Visualizer Panel.

Amphiphilic Moment Panel Features

Use structures from option menu

Choose the structure source for the amphiphilic moment calculation.

  • 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.
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. The file must be in Maestro format.

Job toolbar

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

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

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