:orphan: true

.. _autodock-autodock4-docking:

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AutoDock4 Docking
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This protocol uses `AutoDock4: <https://autodock.scripps.edu/download-autodock4/>`_ tool to predict the binding poses for a set of small molecules over the receptor. 

The search parameters can be modified to make a full use of the AutoDock4 options.

The input can either be an ``AtomStruct`` (to perform the docking on the whole protein) or a ``SetOfStructROIs`` (to perform the docking only on the Structural Regions Of Interest).

Input
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.. include:: ../../../templates/plugins/input-help.rst

.. image:: ../../../../_static/images/plugins/autodock/autodock4-docking/form_1.png
   :alt: AutoDock4 Docking form 1
   :height: 400
   :align: center

|

.. image:: ../../../../_static/images/plugins/autodock/autodock4-docking/form_2.png
   :alt: AutoDock4 Docking form 2
   :height: 400
   :align: center

|

The results of these protocols are a ``SetOfSmallMolecules``, containing the predicted binding poses for the input molecules. 
The user can visualize them using **Analyze Results**, which will display the General SmallMolecules viewer.

A section for defining flexible receptor residues is included in these docking protocols.

.. |testCommand| replace:: autodock.tests.test_autodock.TestAutoDock
.. include:: ../../../templates/plugins/protocol-test.rst