358c4-PosePredictionProtocol.txt

Name

GOLD/AUTODOCK VINA

Software

GOLD/AUTODOCK VINA/SCHRODINGER

System Preparation Parameters

(prepwizard) -propka_pH 7.5 (prepwizard) -fillsidechains -s (ligprep) -adjust_itc -ph 7.0

System Preparation Method

Maestro's prepwizard was used to optimize the protein with pH value and fillsidechains option. Maestro's ligprep was used to generate optimized 3d structure of ligands from 2d structure.

Pose Prediction Parameters

autoscale = 1.5; floodfill_center = cavity_from_ligand 10 atoms; gold_fitfunc_path = plp # use ChemPLP as scoring function to generate poses; num_poses = 200 # generate 200 poses as pose_pool for each complex

Pose Prediction Method

PHE211 and PHE70 are set as flexible. AutoDock Vina is used to rescore the poses.

Answer 1

No

Answer 2

No