1147-1-2deae-PosePredictionProtocol.txt

Name

Minimal Pose Prediction

Software

Flare 2.0 revision 34140

System Preparation Parameters

Assumed pH 4.5

System Preparation Method

Ligands were read from smiles files with Flare, protonated to a pH of 4.5 and minimised with Flare. They were then docked to, 5QC1 accepting the best scoring docking pose according to Lead Finder VSscore.

Pose Prediction Parameters

default of fkcombu

Pose Prediction Method

Summed up above and in the ScoringProtocol text file.

Answer 1

no

Answer 2

Yes

1147-2-jr6hj-LigandScoringProtocol.txt

Name

Scoring with Flare

Software

Flare 2.0 revision 34140

Parameters

Quality Extra Precision
Max Poses 3
Pool Size 1
Population Size 1
Minimize Ligands before docking
Rotate amide bonds
Rotate ester Bonds
Rotate Conjugate bonds heuristically decide

Method

5QC1 and all ligands were loaded into Flare. A docking grid based on the ligand of 5QC1 was retained. All crystal waters were kept in the docking box. The docking calculation was started with above parameters. The scoring was done based on the Lead Finder Virtual screen score and written to file. Ranking and energies were taken from the poses with the lowest LF VSscore.

Answer 1

no

Answer 2

no