.. _sphx_glr_examples_gallery_structure_alphabet:

Structural alphabets
--------------------


.. raw:: html

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

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example we perform a structural alignment of multiple lysozyme variants from different organisms. A feasible approach to perfrom such a multiple structure alignment is the usage of a structural alphabet: At first the structure is translated into a sequence that represents the structure. Then the sequences can be aligned with the standard sequence alignment techniques, using the substitution matrix of the structural alphabet.">

.. only:: html

  .. image:: /examples/gallery/structure/alphabet/images/thumb/sphx_glr_msa_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_alphabet_msa.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Multiple Structural alignment of orthologous proteins</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The following script implements a protein structure search algorithm akin to foldseek VanKempen2024. It harnesses the 3Di alphabet to translate 3D structures into a sequences. Structurally homologous regions between these 3Di sequences can be identified quickly using k-mer matching followed by ungapped seed extension and finally gapped alignment.">

.. only:: html

  .. image:: /examples/gallery/structure/alphabet/images/thumb/sphx_glr_structure_search_thumb.png
    :alt:

  :ref:`sphx_glr_examples_gallery_structure_alphabet_structure_search.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Searching for structural homologs in a protein structure database</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /examples/gallery/structure/alphabet/msa
   /examples/gallery/structure/alphabet/structure_search