Receptor preparation tutorial

The first step in using FRED, HYBRID or POSIT is the creation of an OEDocking receptor, which is a collection of docking related information connected to a protein. A typical receptor is shown in the figure OEDocking receptor and typical docking information below.

OEDocking receptor

OEDocking receptor and typical docking information

There is an automated way to preparing OEDocking receptor files, using SPRUCE. Alternatively, the graphical utility MakeReceptor provides an interactive approach for flexible and customizable receptor preparation.

Interactive modification of a receptor

The MakeReceptor GUI can be used to examine/modify a previously created receptor. The GUI can be used if a user wants to define constraints or include specific water molecules in the receptor. The current implementation of make_receptor takes in a traditional OEBinary formatted receptor (.oeb or .oeb.gz) and will write the newer OEDesignUnit file (.oedu) for input to any of the OEDocking applications. The conversion between the two file types can be done using OEDocking utility programs OEB2DUReceptor and DU2OEBReceptor. For example:

> du2oebreceptor -in rec_5TMG.oedu -out rec_5TMG.oeb.gz
> oeb2dureceptor -in rec_5TMG.oeb.gz -out converted_rec_5TMG.oedu

The OEBReceptor files such as rec_5TMG.oeb.gz can be visualized using VIDA and the components are shown in figure OEDocking receptor and components in VIDA.

OEDocking OEBReceptor

OEDocking receptor and components in VIDA

This OEDocking receptor includes the protein structure and a description of the binding site. This description includes a so called outer contour (highlighted in List Window) which limits the extent of where heavy atoms are to be placed during FRED, HYBRID or POSIT ’s search procedures.

See the MakeReceptor section for generating receptor from structure coordinates instead of from previously generated OEDocking receptor files.