Docking Poses

Pose View

Best poses

After docking finished, you can view the best docked poses for each receptor and ligand in pose table.

bestpose

The best pose table contains receptor name, ligand name, affinity (or free binding energy), RMSD score, logKi and some metrics.

Calculation of logKi

The Ki millimolar (mM) to yoctomolar (yM) will be converted to Molar (M). And then, calculate the log10 of Molar.

Calculation of Metrics

LE

Ligand efficiency

-∆G/N

SILE

size-Independent Ligand efficiency

-∆G/(N^0.3)

FQ

Fit Quality

LE/(0.0715+7.5328/N+25.7079/(N^2) -361.4722/(N^3))

LLE

Lipophilic ligand efficiency

-log⁡Ki-log⁡P

LELP

Ligand Efficiency dependent Lipophilicity

log⁡P/LE

where ΔG is the free energy of binding, N is the number of heavy atoms (non-hydrogen atoms) of ligand, Ki is estimated inhibition constant, logP is the calculated octanol-water partition coefficient

Job poses

In addition to best poses, the Dockey also allows you to view poses for each docking job. You can click a job in job table, a new tab named ligand vs receptor will be display in pose panel.

jobpose

Pose exporting

The best pose table and job pose table has right-click menu that helps you to export the poses.

posemenu

  1. Save Selected Pose: Export current selected pose to a pdb file

  2. Save All Poses: Export all poses to a pdb file

  3. Save Receptor Ligand Complex: Export compound containing receptor and ligand to a pdb file

  4. Export Table: Export current table to CSV file

  5. View Details: View the details of pose including Ki.

Pose Visualization

You can click one pose in best pose table or job pose table to view the 3D structure of ligand-receptor complex in PyMOL view.

poseview

  1. Go to File menu -> Export As Image to save the 3D structure in PyMOL view to PNG file.

  2. Go to File menu -> Export As File to save the content of PyMOL view to pdb file.

Preset Active Binding Sites

Before starting docking, you can right click a receptor in molecular list and then go to menu Preset Active Binding Sites to open a dialog. You can select several residues as active binding sites to see whether ligands can be docked to them. If the ligand can be docked to preset binding sites, the pose in table will has green background color.

posegreen

You can right click the pose with green background, and go to view details to view interactions.

poseinter