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 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.

SPRUCE (Recommended)

The SPRUCE application provides functionality for automated biomolecule preparation for modeling applications. The preparation functions include tautomer evaluation, charge normalization, receptor grid generation and missing protein loop building. A typical receptor generation session could begin with the retrieval of a set of coordinates and an experimental electron density map from the PDB (in this case the RCSB) directly. To automatically retrieve the data files from the PDB, the GetStructure utility in SPRUCE can be given a four character accession code.

For example, to retrieve the PDB entry 5TMG:

> getstructure 5TMG

The above command downloads 5tmg.pdb, 5tmg.cif, 5tmg.mtz files from RCSB database directly. Once the files have been downloaded, SPRUCE can be used to generate DesignUnit (DU) and the rest of the receptor components. The concept of DU and relevant details can be found in the Theory part of SPRUCE.

> spruce -in 5tmg.cif -map 5tmg.mtz

The above command creates the following intermediate DU files:

• 5TMG_A__DU__7EK_A-402.oedu

• 5TMG_B__DU__7EK_B-402.oedu

DU files are generated for each of the monomers in the crystallographic asymmetric unit, in this example there are two copies in the asymmetric unit. If the user has supplied the electron density map (in this example 5tmg.mtz) to the spruce command, the quality of the structure is evaluated using the Iridium protocols.

When there is no bound ligand detected, an error message is written into spruce_output.log. The parameter enumsites -site_residue is required to specify a protein residue in the active site for apo structures.

To create OEDocking receptor files readily used as docking input:

> receptorindu -in 5TMG_A__DU__7EK_A-402.oedu -out rec_5TMG.oedu

The above command then creates receptor inside DU rec_5TMG.oedu as input receptor file for FRED, HYBRID and POSIT.

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 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.