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Fast Rigid Exhaustive Docking | ||||
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Fast Rigid Exhaustive Docking | ||||
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Examples in this section deal with adjusting how FRED docks ligands (i.e. how it determines the pose, or poses if alternate poses are requested, of a ligand within the active site). None of the examples in this section address how the final ligand pose(s) are scored and outputted to the hitlist(s). Hence the same set of output files are returned in each example, the docked structures thus the scores of the outputted ligands will be different however (since these examples adjust how FRED generates the poses to score). The next section has examples of adjusting the final scoring and hitlists.
See section 4.2 for a general explanation of how FRED docks ligands.
fred -dbase my_poses.mol2 -rec my_receptor.oeb.gz -no_dock -opt none
Using this command line FRED will assume that the ligand molecules passed to -dbase are already positioned within the active site, and rescore and re-rank the ligands using the default scoring function Chemgauss3 (see section 4.3.5) since we have not specified a scoring function to use.
-dbaseThis specifies the poses to read in for rescoring and reranking.
-recSpecifies the receptor site to score the ligands in.
-no_dockThis flag tells FRED to skip the exhaustive search (which is how poses are initially generated).
-opttells FRED not to perform solid body optimization on the poses that are passed in.
setup.txt
receptor.oeb.gz
status.txt
chemgauss3_docked.oeb.gz
chemgauss3_scores.txt
fred -dbase my_ligands.oeb.gz \
-rec my_receptor.oeb.gz \
-exhaustive_scoring plp \
-opt plp
The initial exhaustive search to generate candidate poses and the optimization step both have settings for the scoring functions they use to rank or optimize poses respectively. The default scoring function for these operations is Chemgauss3 (see section 4.3.5), however both operations can be set to use different scoring functions as shown in this example which sets both the exhaustive scoring and optimization scoring functions to PLP (see section 4.3.3).
-dbaseThis 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).
-recThis specifies a receptor file to dock the ligands to. 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.
-exhaustive_scoringSets the exhaustive scoring function to PLP.
-optSets the optimization scoring function to PLP.
Note that -exhaustive_scoring and -opt are independent (i.e. you can specify one without the other).
setup.txt
receptor.oeb.gz
status.txt
chemgauss3_docked.oeb.gz
chemgauss3_scores.txt
fred -dbase my_ligands.oeb.gz \
-rec my_ligands.oeb.gz \
-pose_select_weight_shapegauss 1 \
-pose_select_weight_plp 0 \
-pose_select_weight_Chemgauss2 1 \
-pose_select_weight_Chemgauss3 4 \
-pose_select_weight_Chemscore 0 \
-pose_select_weight_oeChemscore 2 \
-pose_select_weight_screenscore 0 \
-pose_select_weight_cgo 0
Once candidate poses have been generated by the exhaustive search and optimization step FRED selects a single best pose from the set of candidates. This pose is then scored and the score is used to rank ligands in the output hitlist. The consensus structure step allows multiple scoring functions to vote for the best docked structure in a rank-by-vote approach. This example shows how to adjust the weight of each scoring function's vote.
-dbaseThis 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).
-recThis specifies a receptor file to dock the ligand to. 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.
-pose_select_weight_shapegaussGives shapegauss a weight of 1 for consensus structure voting.
-pose_select_weight_plpGives PLP a weight of 0 for consensus structure voting (i.e. PLP is ignored for consensus structure).
-pose_select_weight_Chemgauss2Gives Chemgauss2 a weight of 1 for consensus structure voting.
-pose_select_weight_Chemgauss3Gives Chemgauss3 a weight of 4 for consensus structure voting.
-pose_select_weight_ChemscoreGives Chemscore a weight of 0 for consensus structure voting (i.e. Chemscore is ignored for consensus structure).
-pose_select_weight_oeChemscoreGives OEChemscore a weight of 2 for consensus structure voting.
-pose_select_weight_screenscoreGives Screenscore a weight of 0 for consensus structure voting (i.e. Screenscore is ignored for consensus structure).
-pose_select_weight_cgo
setup.txt
receptor.oeb.gz
status.txt
chemgauss3_docked.oeb.gz
chemgauss3_scores.txt
fred -dbase my_ligands.oeb.gz \
-rec my_ligands.oeb.gz \
-pose_select_weight_shapegauss 0 \
-pose_select_weight_plp 0 \
-pose_select_weight_Chemgauss2 0 \
-pose_select_weight_Chemgauss3 0 \
-pose_select_weight_Chemscore 0 \
-pose_select_weight_oeChemscore 0 \
-pose_select_weight_screenscore 0 \
-pose_select_weight_cgo 0
This example disables the consensus structure step by setting all the scoring function weights for consensus structure to zero. In this case the top ranked pose from the optimization step (or from the exhaustive search if optimization is also disabled) will scored with Chemgauss3 and outputted to the hitlist(s).
-dbaseThis 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).
-recThis 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.
-pose_select_weight_shapegaussGives shapegauss a weight of 0 for consensus structure voting.
-pose_select_weight_plpGives PLP a weight of 0 for consensus structure voting.
-pose_select_weight_Chemgauss2Gives Chemgauss2 a weight of 0 for consensus structure voting.
-pose_select_weight_Chemgauss3Gives Chemgauss3 a weight of 0 for consensus structure voting.
-pose_select_weight_ChemscoreGives Chemscore a weight of 0 for consensus structure voting.
-pose_select_weight_oeChemscoreGives OEChemscore a weight of 0 for consensus structure voting.
-pose_select_weight_screenscoreGives Screenscore a weight of 0 for consensus structure voting,
-pose_select_weight_cgoGives CGO a weight of 0 for consensus structure voting.
setup.txt
receptor.oeb.gz
status.txt
chemgauss3_docked.oeb.gz
chemgauss3_scores.txt
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Fast Rigid Exhaustive Docking | ||||
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