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.
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.
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.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 -in 5tmg.cif -map 5tmg.mtz
The above command creates the following intermediate DU files:
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
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
enumsites -site_residue is required to specify a protein residue in the active site for apo
To create OEDocking receptor files readily used as docking input:
> receptorindu -in 5TMG_A__DU__7EK_A-402.oedu -out rec_5TMG.oedu
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.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.
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.