Edit a Receptor

Context

Receptors are specialized versions of protein structures that identify the binding site on the protein and optionally specify constraints that must be satisfied by molecule docked into the site. Orion currently supports automatic generation of receptors using the spruce prep floes (see the Dock One Million Molecules with Gigadock Floe tutorial for an example), but not editing of the receptor to adjust the location of the active site or add/remove constraints. However, the receptor can be downloaded to a local machine and edited with the make_receptor GUI app that is part of OpenEye’s OEDocking package (this requires an OEDocking license) and the re-uploaded to Orion for use with the Gigadock floe. This howto explains this process.

Procedure

  1. Find the Gigadock floe and launch it with the following settings

    • Job Properties

      • Output Path : Choose an appropriate output path

    • Promoted Parameters

      • Inputs

        • Receptor Dataset Set this to the dataset with the receptor/design-unit to be edited.

  2. Wait for the floe to finish. This will happen quickly as the floe was given no molecule to dock.

  3. Locate the ‘Receptor’ dataset created by the floe.

  4. Download the ‘Receptor’ dataset as a .oeb file to the local machine.

  5. Use the make_receptor GUI app to edit the receptor. (see here)

  6. Save the receptor as an .oedu file and close the make_receptor GUI.

  7. In Orion go to the Data page and upload the .oedu file from the previous step as a dataset.

The upload .oedu dataset can be used with the Gigadock floe (and other floes that require a receptor / design unit).