Tutorials
==========================

This section contains step-by-step tutorials to familiarise users with all aspects of running PELE software,
from protein preparation to analysis of output files.

We assume you have already installed the software and have access to Schrödinger Maestro.

    - `Disturbing protein-protein interaction between a bromodomain and a histone <ppi.html>`_
    - `Glide docking pose refinement in hemagglutinin binding site <induced_fit.html>`_
    - `GPCR simulation of BU72 agonist of the μ-opioid receptor <gpcr.html>`_
    - `Performing a fragment growing simulation in p38 kinase <frag_pele.html>`_
    - `Pocket exploration and comparison to the native pose by calculating RMSD <site_finder.html>`_
    - `Creating custom plots with built-in Plotter <plotter.html>`_
    - `Ligand parametrization using peleffy <peleffy.html>`_
    - `Binding simulation of a JAK-2 kinase <out_in.html>`_

For further information about the obtained outputs files, refer to `this page <outputs.html>`_.

.. toctree::
   ppi.rst
   :hidden:

.. toctree::
   induced_fit.rst
   :hidden:

.. toctree::
   gpcr.rst
   :hidden:

.. toctree::
   frag_pele.rst
   :hidden:

.. toctree::
   site_finder.rst
   :hidden:

.. toctree::
   outputs.rst
   :hidden:

.. toctree::
   plotter.rst
   :hidden:

.. toctree::
   peleffy.rst
   :hidden:

.. toctree::
   out_in.rst
   :hidden: