:orphan: true .. _autodock-vina-docking: ############################################################### Vina Docking ############################################################### This protocol uses `AutoDock Vina: <https://vina.scripps.edu/>`_ docking engine to predict the binding poses for a set of small molecules over the receptor. Currently, `Vina 1.2 <https://github.com/ccsb-scripps/AutoDock-Vina>`_ is included. 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 ---------------------------------------- .. include:: ../../../templates/plugins/input-help.rst .. image:: ../../../../_static/images/plugins/autodock/vina-docking/form.png :alt: Vina Docking :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.TestVina .. include:: ../../../templates/plugins/protocol-test.rst