.. _sphx_glr_examples_gallery_structure_modeling:

Molecular dynamics and docking
------------------------------


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    <div class="sphx-glr-thumbnails">


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use AutoDock Vina Trott2010 from within Biotite for docking a ligand ...">

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  .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_docking_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_modeling_docking.py`

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      <div class="sphx-glr-thumbnail-title">Docking a ligand to a receptor</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we will analyze a trajectory of a Gromacs MD simulation: The trajectory contai...">

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  .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_md_analysis_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_modeling_md_analysis.py`

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      <div class="sphx-glr-thumbnail-title">Basic analysis of a MD simulation</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how the BinaryCIF format can be used as an alternative to classical t...">

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  .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_mmtf_trajectory_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_modeling_mmtf_trajectory.py`

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      <div class="sphx-glr-thumbnail-title">BinaryCIF as trajectory format</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The elastic network model (ENM) is a fast method to estimate movements in a protein structure, ...">

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  .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_normal_modes_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_modeling_normal_modes.py`

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      <div class="sphx-glr-thumbnail-title">Visualization of normal modes from an elastic network model</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This script creates rotamers for an amino acid, by randomly rotating about all rotatable bonds....">

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  .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_rotamer_library_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_modeling_rotamer_library.py`

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      <div class="sphx-glr-thumbnail-title">Creation of an amino acid rotamer library</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Based on a 10 ns Gromacs MD simulation of 0.15 mM sodium chloride, the distance of solvation sh...">

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  .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_solvation_shells_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_modeling_solvation_shells.py`

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      <div class="sphx-glr-thumbnail-title">Analysis of solvation shells</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This script displays positional changes of secondary structure elements (SSE) in the course of ...">

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  .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_trajectory_sse_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_modeling_trajectory_sse.py`

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      <div class="sphx-glr-thumbnail-title">Secondary structure during an MD simulation</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In selective sodium/potassium channels, the internal cavity of the pore is walled off from the ...">

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  .. image:: /examples/gallery/structure/modeling/images/thumb/sphx_glr_water_exchange_noexec_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_modeling_water_exchange_noexec.py`

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      <div class="sphx-glr-thumbnail-title">Cavity solvation in different states of an ion channel</div>
    </div>


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    </div>


.. toctree::
   :hidden:

   /examples/gallery/structure/modeling/docking
   /examples/gallery/structure/modeling/md_analysis
   /examples/gallery/structure/modeling/mmtf_trajectory
   /examples/gallery/structure/modeling/normal_modes
   /examples/gallery/structure/modeling/rotamer_library
   /examples/gallery/structure/modeling/solvation_shells
   /examples/gallery/structure/modeling/trajectory_sse
   /examples/gallery/structure/modeling/water_exchange_noexec