Membrane Permeability Panel

Calculate the passive membrane permeability of a set of congeneric ligands.

To open this panel: click the Tasks button and browse to ADME and Molecular Properties → Physics-Based Membrane Permeability.

  • Using
  • Features
  • Additional Resources

Using the Membrane Permeability Panel

This panel allows you to calculate the passive membrane permeability of a set of molecules. It is primarily intended for use on congeneric series of ligands to evaluate the relative permeability of similar ligands.

The membrane permeability facility has a special sampling method for macrocycles, which is used automatically.

The calculations can take several minutes per molecule. The molecules should be all-atom 3D structures in a reasonable geometry. You can use LigPrep to convert 2D structures or SMILES strings to 3D structures.

The main results of the calculation are the structures of the ligands in the conformation that is predicted to be the most likely conformation inside the membrane, some Maestro free energy properties, given in kcal/mol, and the logarithm of the predicted RRCK permeability in cm/s. See Membrane Permeability for information on these properties.

You can visualize the contributions to the Membrane HDLD property by atom in the Prime Energy Visualizer Panel. See Membrane Permeability for instructions.

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

structurebased_adme permeability structure_file

See Running Schrödinger Applications from the Command Line for information on running jobs from the command line, and structurebased_adme permeability Command Help for command options.

Membrane Permeability Panel Features

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.
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.

Skip sampling option

Skip the conformational sampling stage. This option is useful if you provide membrane-appropriate conformations as input.

Job toolbar

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

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

Tutorials

Related Topics