4.1 Input

FRED takes the following input

Multiconformer ligand database

This is a file or files with multiconformer expansions of the ligands FRED will dock. FRED has been validated using conformer databases produced with the OpenEye conformer generator OMEGA. Other conformer generators that produce output in a format readbale by FRED are also permissible.

Receptor file

This is a special type of .oeb file (OEB is OpenEye's standard molecule file format) which describes the receptor site to FRED.

A receptor file always contains the following:

The structure of the target protein.
The location of the receptor site on the protein.
A shape potential grid that describes the shape complementarity of the active site.

Additionally a receptor file may contain:

One or two isocontour levels of the shape potential grid which create shapes complementary to the active site.
The structure of a known bound ligand.
Docking constraints.

The receptor file can be created by using the FRED command line executable or a stand-alone GUI (fred_receptor) which is designed to created and edit receptor files.

Command line arguments

Which can also be entered in a parameter file.

				FRED Fast Rigid Exhaustive Docking

				FRED Fast Rigid Exhaustive Docking