:orphan: true

.. _autodock-autodockGPU-docking:

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AutoDock-GPU Docking
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This protocol uses `AutoDock-GPU: <https://github.com/ccsb-scripps/AutoDock-GPU>`_, the GPU implementation of AutoDock, which is several times faster and includes many bug fixes and new features. 

It includes different parameters than AutoDock4, so it has been moved to a new protocol.

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).

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

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.. image:: ../../../../_static/images/plugins/autodock/autodockGPU-docking/form_2.png
   :alt: AutoDock-GPU 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.TestAutoDockGPU
.. include:: ../../../templates/plugins/protocol-test.rst