grandconsen_qpld_XP_SP_Vina_AD4
Schrodinger2016,Vina1.1.2,Autodock4.2.5
Assumed pH 7.4
We used Maestro's prepwizard to add hydrogens using default parameters
and an assumed pH of 7.4.
The binding site HIS 451 was used in an alternative flipped, "open", doubly protonated (HIP) configuration.
Ligand conformational libraries were generated using ligprep.
A grand consensus was then used (averages) employing the scores and ranks for each program and scoring function, that is, qpld (quantum polarized ligand docking), Glide Xp, Glide SP, Autodock Vina, and Autodock4 Binding energy.
In this submission, ligands are ranked according to average score
qpld_XP_vina
Schrodinger2016,Vina1.1.2
Assumed pH 7.4
Maestro's prepwizard was used to add hydrogens using default parameters.
All the waters were retained
The binding site residue HIS 451 was used in a flipped, and "open" alternative configuration, and doubly protonated (HIP)
Ligand conformational libraries were generated using LigPrep.
Preparation for docking with Vina was done using MGLTools with the ligand pdb files from ligprep.
Exhaustiveness=32 #exhaustiveness of global search (default=8)
Poses were predicted using the deepest energy pose from qpld, and where this did not produce a pose, then either XP poses were used (FXR_16), or Vina poses (FXR_65, 79, 80, 97, and 101)