Docking Poses
=============

Pose View
---------

Best poses
~~~~~~~~~~

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

.. rst-class:: wy-text-center

	|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**

.. list-table::

	* - 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.

.. rst-class:: wy-text-center

	|jobpose|

Pose exporting
--------------

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

.. rst-class:: wy-text-center

	|posemenu|

#. **Save Selected Pose**: Export current selected pose to a pdb file
#. **Save All Poses**: Export all poses to a pdb file
#. **Save Receptor Ligand Complex**: Export compound containing receptor and ligand to a pdb file
#. **Export Table**: Export current table to CSV file
#. **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.

.. rst-class:: wy-text-center

	|poseview|

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

.. rst-class:: wy-text-center

	|posegreen|

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

.. rst-class:: wy-text-center

	|poseinter|


.. |bestpose| image:: _static/bestpose.png

.. |jobpose| image:: _static/jobpose.png

.. |posemenu| image:: _static/posemenu.png
	:width: 250

.. |poseview| image:: _static/poseview.png
	:width: 500

.. |posegreen| image:: _static/posegreen.png
	:width: 500

.. |poseinter| image:: _static/poseinter.png
	:width: 500