PDB2RECEPTOR tutorial

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

OEDocking receptor

OEDocking receptor and typical docking information

An OEDocking receptor includes the protein structure and a description of the binding site. This description includes a so called outer contour that indicates where heavy atoms are to be placed during FRED, HYBRID or POSIT ’s search procedures.

A pose receptor traditionally includes a bound ligand used to help identify existing binding modes, and may include so called extra molecules which are interesting items such as waters and solvents that have been stripped for the purposes of docking.

While there are several ways to make receptors, POSIT has a simplified, easy to use command line utility, Pdb2Receptor.

The most complicated portion of making pose receptors is identifying the bound ligands. If Pdb2Receptor is run with only an input protein file, it outputs a list of potential ligands and halts unless only one valid ligand is detected in which case a receptor is created with that ligand:

> pdb2receptor –pdb 2IKO.pdb.gz

Executing this command will create a receptor with the one detected ligand (with residue 7IG601A). The same receptor could also have been created by explicitly listing the residue on the command line.

> pdb2receptor –pdb renin/2IKO.pdb.gz -ligand_residue 7IG601A -receptor 2IKO_receptor.oeb.gz

This command creates the following files:

  • 2IKO_receptor.oeb.gz - the OEDocking receptor

See the Pdb2Receptor section for more details, including how to more explicitly control output file names.