Subsections

6.4 Scoring

By default FRED outputs a Chemgauss3 hitlist which has the top 1000 ligands as scored by Chemgauss3. This section has examples of how to have FRED use other scoring functions to ranks ligands.

6.4.1 One scoring function

6.4.1.1 Command Line

fred -dbase my_ligands.oeb.gz -rec my_receptor.oeb.gz -plp -hitlist_size 5000

FRED will maintain and output a hitlist which uses the PLP scoring function, in place of the default Chemgauss3 scoring function. This example also increases the size of the hitlist to 5000, from the default value of 1000.

-dbase

my_ligands.oeb.gz

This tells FRED where the ligands it is going to dock are, in this case the file my_ligands.oeb.gz. The ligand file should have multiple conformers of all flexible ligands (see section 5.5 for more detail on preparing the ligand database).

-rec

my_receptor.oeb.gz

This specifies a receptor file to dock to the ligand too. The receptor file

must be created prior to running FRED with this command line. This file can be created by FRED or by the fred_receptor GUI.

-plp

Enables plp output hitlist.

-hitlist_size

5000

Tells FRED to keep and output the top 5000 ligands in the PLP hitlist.

6.4.1.4 Output

setup.txt: A file with the settings of all of FRED's parameters. Note that there will be many more parameters in this file than those specified on the command line because many parameters have default values. This file will be written at the beginning of the run.
receptor.oeb.gz: This file contains a copy of the receptor site used for the run. This file will be written at the beginning of the run.
status.txt: This file will be written every few seconds by FRED and indicates the status of the run.
plp_docked.oeb.gz: contains the structure of the top 5000 docking ligands as ranked by PLP.
plp_scores.txt: list the names, scores and SMILES representation of the top 5000 docked ligands as ranked by PLP in a text format.

6.4.2 Multiple scoring functions

6.4.2.1 Command Line

fred -dbase my_ligands.oeb.gz \
     -rec my_receptor.oeb.gz \
     -plp \
     -chemgauss3 \
     -shapegauss \
     -oechemscore \
     -screenscore \
     -hitlist_size 5000

6.4.2.2 Description

This example enables multiple scoring functions and output hitlists and increases the size of the output hitlists to 5000, from the default value of 1000. Also because multiple scoring functions are enabled FRED will also automatically maintain a consensus scoring hitlist using all the selected scoring functions.

6.4.2.3 Parameters

-dbase

my_ligands.oeb.gz

-rec

my_receptor.oeb.gz

This specifies a receptor file to dock to the ligand too. The receptor file must be created prior to running FRED with this command line. This file can be created by FRED or by the fred_receptor GUI.

-hitlist_size

5000

Tells FRED to keep and output the top 5000 ligands in the PLP hitlist.

-plp

Enables PLP output hitlist.

-chemgauss3

Enables Chemgauss3 output hitlist.

-oechemscore

Enables OEChemscore output hitlist.

-screenscore

Enables Screenscore output hitlist.

6.4.2.4 Output

setup.txt: A file with the settings of all of FRED's parameters. Note that there will be many more parameters in this file than those specified on the command line because many parameters have default values. This file will be written at the beginning of the run.
receptor.oeb.gz: This file contains a copy of the receptor site used for the run. This file will be written at the beginning of the run.
status.txt: This file will be written every few seconds by FRED and indicates the status of the run.
plp_docked.oeb.gz: contains the structure of the top 5000 docking ligands as ranked by PLP.
plp_scores.txt: list the names, scores and SMILES representation of the top 5000 docked ligands as ranked by PLP in a text format.
chemgauss3_docked.oeb.gz: contains the structure of the top 5000 docking ligands as ranked by Chemgauss3.
chemgauss3_scores.txt: list the names, scores and SMILES representation of the top 5000 docked ligands as ranked by Chemgauss3 in a text format.
oechemscore_docked.oeb.gz: contains the structure of the top 5000 docking ligands as ranked by OEChemscore.
oechemscore_scores.txt: list the names, scores and SMILES representation of the top 5000 docked ligands as ranked by OEChemscore in a text format.
screenscore_docked.oeb.gz: contains the structure of the top 5000 docking ligands as ranked by Screenscore.
screenscore_scores.txt: list the names, scores and SMILES representation of the top 5000 docked ligands as ranked by Screenscore in a text format.
consensus_docked.oeb.gz: contains the structure of the top 5000 docking ligands as ranked by a consensus score using PLP, Chemgauss3, OEChemscore, and Screenscore (i.e. the selected scoring functions).
consensus_scores.txt: list the names, scores and SMILES representation of the top 5000 docked ligands (in a text format) as ranked by a consensus score using PLP, Chemgauss3, OEChemscore and Screenscore (i.e. the selected scoring functions).