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 offers automatic generation of receptors using the Spruce preparation floes (SPRUCE - Protein Preparation and SPRUCE - Import Prepared PDB Files Floes). The View Prepared Design Unit/Receptor section of the Dock One Million Molecules with Gigadock Floe tutorial shows an example. Also available in Orion is the ability to directly edit the receptor to adjust the location of the active site and to add, remove, and edit constraints.

Note

Please see the Edit DU Receptor section of the 3D & Analyze page documentation in the User Guide for a complete description of this feature.

Alternate Procedure

The tools within Orion offer the most direct way to edit receptors and constraints.

However, if desired, the receptor and constraints can be edited outside of Orion. This requires downloading the receptor and editing it with the Make Receptor GUI utility in the OEDocking Application and then re-uploading it to Orion for use with the Gigadock Floe.

  1. Launch the Gigadock Floe with the input Receptor Dataset set to the dataset with the receptor/design unit to be edited.

  2. The floe will finish quickly as it was not given a molecule to dock.

  3. Locate the receptor dataset created by the floe and download it as an .oeb file.

  4. Use the Make Receptor GUI Application to edit the receptor. Notice that many controls for the GUI are very similar to those used in Orion.

  5. Save the receptor as an .oedu file and close the Make Receptor GUI.

  6. In Orion, go to the Data page and upload the .oedu file as a dataset. This can be used with any floe that requires a receptor / design unit.