:orphan:

.. status publishable
.. product Docking
.. sectionauthor Clive
.. SME Clive
.. PR Dave
.. TW Ken
.. date 2018

.. _dockingDTS:

|medea| |docking| Create Host-Guest and Surface-Guest Models
------------------------------------------------------------
.. admonition:: **At-a-Glance**

   |medea|\ :sup:`®`\ [#TM]_ |docking| automatically creates, adjusts, and
   refines host-guest and surface-guest systems. Employing
   the well-known Metropolis Monte Carlo algorithm [#Metropolis1953]_,
   |medea| |docking| evaluates van der Waals interactions to
   generate and assess stable system configurations. The
   resulting host-guest structures may then be employed in forcefield
   and first-principles based simulations. |medea| |docking| can
   be invoked interactively within the |medea| |menvironment|
   or by using |medea| |mflowcharts| on the JobServer. |medea| |docking|
   is a building tool that allows you to
   combine systems automatically to create the starting points
   for further simulation studies.

   **Key Benefits**

   * Saves time through accelerated and automated model construction and refinement
   * Simplifies automated Flowchart based model construction for screening, allowing construction of host-guest and surface-guest systems without interactive manipulation
   * Explores multiple guest configurations, searching and evaluating many possible binding configurations


.. figure:: /Datasheets/images/EthanolTheta1.png
   :width: 1.8in
   :align: center

   Alcohol molecules docked in a microporous material using |medea| |docking|.


Key Features
^^^^^^^^^^^^

* Automatic combination of host and guest structures
* Minimization of steric overlap between host and guest
* Automated energy based refinement of sorbate position and orientation
* Interactive screen updates, and full user control of model view and scale during docking
* Control of simulation length, Monte Carlo temperature, maximum position, and rotation displacements
* Combination of multiple sorbates with host structure
* Employs Metropolis Monte Carlo Algorithm, allowing user control of the employed search (via control of acceptance probability within the temperature setting)
* For use with surface, microporous, and porous materials models

:myquote:`I will say that enzyme and glucoside must fit together like lock and key in order to be able to exercise a chemical action on each other`

:myquotee:`Emil Fischer, 1852-1919`


Required Modules
^^^^^^^^^^^^^^^^
* |medea| |menvironment|
* |medea| |docking|

Related Modules
^^^^^^^^^^^^^^^^^
* |medea| |mlammps| |mstdenv|
* |medea| |mvasp|
* |medea| |mmopac|
* |medea| |mgibbs|
* |medea| |mgaussiangui|


Find Out More
^^^^^^^^^^^^^

To learn more about the use of docking to provide insights
into host-guest interactions in materials science, see
the following papers on the following topics:

.. add for a column break, adjust where needed
.. raw:: latex

   \newpage

* General host-guest interactions [#Catlow1993]_,
* Understanding templating with organic additives [#Lewis1995]_,
* Simulating CFC interactions [#George1996]_, and host-guest
* Interactions in isomerization [#Tschaufeser1999]_.

|
|

.. [#TM] |regTMinfo|

.. [#Metropolis1953] N. Metropolis *et al.*,
   *J. Chem. Phys.* **21**, 1087 (1953)
   (`DOI <https://doi.org/10.1063/1.1699114>`__)

.. [#Catlow1993] C.R.A. Catlow *et al.*,
   *Proc. R. Soc. Lond. A* **442**, 85 (1993)
   (`DOI <https://doi.org/10.1098/rspa.1993.0092>`__)

.. [#Lewis1995] D.W. Lewis *et al.*,
   *J. Phys. Chem.* **99**, 11194 (1995)
   (`DOI <https://doi.org/10.1021/j100028a022>`__)

.. [#George1996] A.R. George *et al.*,
   *Zeolites* **17**, 466 (1996)
   (`DOI <https://doi.org/10.1016/S0144-2449(96)00024-3>`__)

.. full author list: P.T. Tschaufeser and C.M. Freeman
.. [#Tschaufeser1999] P.T. Tschaufeser *et al.*,
   *Catal. Lett.* **60**, 77 (1999)
   (`DOI <https://doi.org/10.1023/A:1019030201752>`__)

.. only:: html

   :download: :download:`pdf </Datasheets/Datasheet-Docking.pdf>`