 |
 |
 | FRED
Fast Rigid Exhaustive Docking | ||||
 |
 |
 |
 |
||||
|
|
| FRED
Fast Rigid Exhaustive Docking | ||||
|
|
|
|
||||
This section has several examples of how to use the FRED executable to create a receptor site. Note that a receptor file can also be created using the fred_receptor GUI available from the download section of the OpenEye website (www.eyesopen.com).
These examples all have FRED create and write a receptor site file and then terminate. If you add the -dbase flag, and pass the name of a multiconformer ligand file to it FRED will begin docking those molecules after creating the receptor site and writing it to a file.
fred -pro protein.pdb -box box.pdb -addbox 4.0
FRED will create a receptor site with the given protein, using a user supplied box to locate the site on the protein.
-proThis tells FRED to create a receptor using the protein located in the file protein.pdb. If the protein structure contains a bound ligand it should be stripped from the file before running FRED.
-boxThis flag defines the extents of the active site using a box that is in a molecular file format. The maximum and minimum x,y and z values of any heavy atom in box.pdb will define the maximum and minimum x,y and z values of the box, which is always aligned along the coordinate axises.
-addboxThis flag tells FRED to modify the box specified by the -box flag, by adding 4 Angstroms to every side. This flag is optional, but it very commonly used with this setting when box.pdb is a bound ligand. (passing a bound ligand to -box without using -addbox flag generally results in the receptor site being too small).
setup.txt
status.txt
receptor.oeb.gz
fred -pro protein.pdb -bound_ligand bound_ligand.pdb
FRED will create a receptor site, by using the supplied protein structure in combination with a shape based site detection algorithm and the position of a known bound ligand. The extent of the site created is determined by the site detection algorithm with some guidance from the position of the known bound ligand.
-protells FRED to create a receptor using the protein located in the file protein.pdb. If the protein structure contains a bound ligand it should be stripped from this file before running FRED.
-bound_ligandspecifies a file containing a ligand in a pose bound to the active site (generally from the same x-ray crystallography data used to determine the protein structure). FRED uses this bound ligand in conjunction with a shape based site detection algorithm to determine the extent of the active site.
setup.txt
status.txt
receptor.oeb.gz
fred -pro protein.pdb -box box.pdb -addbox 4.0 -bound_ligand ligand.pdb
FRED will create a receptor site with the given protein, using a user supplied box to locate the site on the protein. FRED will also attach a bound ligand (ligand.pdb) to the receptor site, although because we have specified the -box flag the ligand will not be used to locate the receptor site as was the case in the previous example.
-proThis tells FRED to create a receptor using the protein located in the file protein.pdb. If the protein structure contains a bound ligand it should be stripped from the file before running FRED.
-boxThis flag defines the extents of the active site using a box that is in a molecular file format. The maximum and minimum x,y and z values of any heavy atom in box.pdb will define the maximum and minimum x,y and z values of the box, which is always aligned along the coordinate axises.
-addboxThis flag tells FRED to modify the box specified by the -box flag, by adding 4 Angstroms to every side. This flag is optional, but it very commonly used with this setting when box.pdb is a bound ligand. (passing a bound ligand to -box without using -addbox flag generally results in the receptor site being too small).
-bound_ligandThis flag tells FRED to attach ligand.pdb to the receptor file as a known bound ligand. Because we have specified the -box flag the structure of the bound ligand is not used to locate the receptor site.
setup.txt
status.txt
receptor.oeb.gz
fred -pro protein.pdb
FRED will create a receptor site using the supplied protein and will guess at the location of the active site using a shape based site detection algorithm. This method of setting up a receptor site is not foolproof and it is possible that FRED will not locate the active site correctly. Therefore it is recommended that you use either a bound ligand or specify the location of the active site with a box if that information is available.
Success at determining the active site with this method is fairly binary, i.e. site detection either works well or fails completely. A good rule of thumb is that the active site will be correctly located 4 out of 5 times.
-protells FRED to create a receptor using the protein located in the file protein.pdb. If the protein structure contains a bound ligand it should be stripped from this file before running FRED.
-bound_ligandspecifies a file containing a ligand in a pose bound to the active site (generally from the same x-ray crystallography data used to determine the protein structure). FRED use this bound ligand in conjunction with a shape based site detection algorithm to determine the extent of the active site.
setup.txt
status.txt
receptor.oeb.gz
|
|
| FRED
Fast Rigid Exhaustive Docking | ||||
|
|
|
|
||||