Subsections

5.3 Receptor file

To perform its primary purpose of docking molecules, FRED needs a description of the active site contained in a receptor file (see section 4.1). A stand alone GUI application, fred_receptor, for creating receptor files is available from the OpenEye website's download section, which uses the same license as FRED. It is recommended that you use this application to setup your receptor file, however a receptor file can also be setup using the FRED executable.

5.3.1 File Format

A receptor file always uses a special version of the OEB format (i.e. it will always be an .oeb or .oeb.gz file). FRED and fred_receptor fully support this file format. Other OpenEye programs, including Vida 2.1, only read the target protein structure from this file and cannot currently see the extra receptor specific data in the file.

5.3.2 Querying

The FRED command line executable can list basic properties of a receptor file simply by passing the receptor file to the executable using the -rec flag. The properites listed will be:

The size of the site box.
The size of the output contour (if there is one).
The size of the inner contour (if there is one).
If a bound ligand is present.
The names of any protein constraints and whether they are enabled.
The names of any custom constraints and whether they are enabled.

5.3.2.1 Reasonable contour values

There is no direct limit to the size of an active site, however you should generally expect that the inner contour volume is around 50-100 cubic Angstroms and the outer contour is in the range of 500-2000 cubic Angstroms.

5.3.2.2 Example

ninja:~/TESTING/FRED-docs> fred -rec rec1ppx.oeb.gz

          :jGf:                .o88o.                          .o8
        :jGDDDDf:              888 `'                         '888
      ,fDDDGjLDDDf,           o888oo  oooo d8b  .ooooo.   .oooo888
    ,fDDLt:   :iLDDL;          888    `888""8P d88' `88b d88' `888
  ;fDLt:         :tfDG;        888     888     888ooo888 888   888
,jft:   ,ijfffji,   :iff       888     888     888    .o 888   888
     .jGDDDDDDDDDGt.          o888o   d888b    `Y8bod8P' `Y8bod88P'
    ;GDDGt:''':tDDDG,
   .DDDG:       :GDDG.         Copyright (c) 2003,2004,2005,2006
   ;DDDj         tDDDi         OpenEye Scientific Software, Inc.
   ,DDDf         fDDD,         Licensed to OpenEye Scientific Software
    LDDDt.     .fDDDj          Version: 2.2 (Build date 20060810)
    .tDDDDfjtjfDDDGt           OEChem version: 1.4.2 debug 20060810
      :ifGDDDDDGfi.            Platform: linux-2.6-g++4.1-i586
          .:::.                Supported Run Modes:
  ......................         Single processor
  DDDDDDDDDDDDDDDDDDDDDD         PVM Multiprocessor (PVM Slavename : FRED)
  DDDDDDDDDDDDDDDDDDDDDD

----------------------------------------
#Interface settings

#Receptor Site :
    -rec  rec1ppx.oeb.gz

Writing settings to : setup.txt
Run status will periodically be written to : status.txt

-----Receptor Information-----
  Site box volume      : 2373
  Outer contour volume : 697
  Inner contour volume : 103
  Standard Constraints
    "SER496 HB" is ENABLED
  Writing a copy of the receptor to receptor.oeb.gz

----------------------------------------

5.3.3 GUI Creation

See the documentation that comes with the fred_receptor GUI distribution available from the Downloads section of the OpenEye website.

5.3.4 Command Line Creation

The FRED executable can create a receptor file by passing it a target protein (using the -pro parameter) along with the following additional parameters:

-bound_ligand: FRED will create a receptor file using the supplied target protein, setting up the active site around the bound ligand. The extent of the site will be automatically determined using the bound ligand in combination with a shape based site detection routine (the -addbox flag if supplied is ignored).
-box: FRED will create a receptor file using the supplied target protein and assume that the active site is centered around a box file passed to the -box flag. The format of the box file is any standard molecular format. FRED will create a site box aligned along the x,y and z coordinate axis with maximum and minimum extents equal to the maximum and minimum x, y and z value of any heavy atom in the molecule. If the -addbox flag is specified, each side of the box is extended by the value of the -addbox flag.
-box and -bound_ligand: This works identically to supplying just the -box flag, except that the supplied bound ligand will also be attached to the receptor file.
neither -box nor -bound_ligand: If nothing is known about the location of the protein's active site you can opt to supply only the -pro flag to FRED. In this case FRED will create a receptor and determine the active site using an automatic shape based site detection routine. While this automatic method of determining the active site is fairly effective, it is not foolproof and an independent inspection and verification of the site chosen should be performed before a docking run is undertaken. A good rule of thumb is that the automatic site detection has about an 80% success rate.

Once FRED creates the receptor file it will write out basic information about the receptor to stderr and write the receptor to the file receptor.oeb.gz or <prefix>_receptor.oeb.gz if you have specified the -prefix flag.

If you supplied FRED with a database of ligands to dock, FRED will begin docking those molecules after the receptor has been created and written out, otherwise FRED will terminate.

5.3.4.1 Preparing the protein

Prior to creating a receptor the protein which will be passed to the -pro flag should be prepared as follows:

Bound molecules: Many protein files contain crystallographic waters and other solvent molecules. The user may choose to keep or strip these molecules from the protein file. Any bound molecules present in the protein file will be treated by FRED like any other part of the protein and allowed to interact with docked ligands. Any active molecules bound to the protein active site should be removed from the protein file as they will block ligands from docking into the active site.
Protonation state: The target protein should be properly protonated before being given to FRED. FRED accepts the input protonation state of the protein, except in the cases when the protonation state is not fully specified by the input file (such as with PDB and MOL2 files with implicit hydrogens). In these cases FRED will take a best guess as to the correct protonation state.
Charging protein: Charges are only needed by FRED when using the Zapbind scoring function. By default the FRED will accept the input charges on the protein. However, if the -assign_protein_charges flag is set to true FRED will assign MMFF charges to the protein.

The custom constraints can also be added to the receptor file, see the next section for details.

				FRED Fast Rigid Exhaustive Docking

				FRED Fast Rigid Exhaustive Docking