Protein-related items
---------------------

| :ref:`gmx dssp <gmx dssp>`, :ref:`gmx rama <gmx rama>`,
  :ref:`gmx wheel <gmx wheel>`
| To analyze structural changes of a protein, you can calculate the
  radius of gyration or the minimum residue distances over time (see
  sec. :ref:`rg`), or calculate the RMSD (sec. :ref:`rmsd`).

To analyze the secondary structure of a protein (not only for static
structures, but also for trajectories), you can use the program
:ref:`gmx dssp <gmx dssp>`, which is a native implementation of DSSP
algorithm :ref:`176 <refKabsch83>`, but also is based on the (`DSSP
V.4 algorithm <https://github.com/PDB-REDO/dssp>`__) with some additional
features. For example, you can take into account native hydrogens from
the structure (``-hmode gromacs``, set by default), while in the original
algorithm, hydrogen atoms are set as pseudo-atoms with coordinates based
on the coordinates of the MainChain atoms (``-hmode dssp``). Also, it is
possible to conduct a fast search for neighboring residues using
Neighbor Search (``-nb``, default), instead of the slow enumeration of
protein residues among themselves according to the "each with each"
principle implemented in the original algorithm (``-nonb``).

One other important analysis of proteins is the so-called *Ramachandran
plot*. This is the projection of the structure on the two dihedral
angles :math:`\phi` and :math:`\psi` of the protein backbone, see
:numref:`Fig. %s <fig-phipsi>`: 

.. _fig-phipsi:

.. figure:: plots/phipsi.*
   :width: 8.00000cm

   Definition of the dihedral angles :math:`\phi` and :math:`\psi` of
   the protein backbone.

To evaluate this Ramachandran plot you can use the program
:ref:`gmx rama <gmx rama>`. A typical output
is given in :numref:`Fig. %s <fig-rama>`.

.. _fig-rama:

.. figure:: plots/rama.* 
    :width: 15.00000cm

    Ramachandran plot of a small protein.

When studying :math:`\alpha`-helices it is useful to have a *helical
wheel* projection of your peptide, to see whether a peptide is
amphipathic. This can be done using the :ref:`gmx wheel <gmx wheel>`
program. Two examples are plotted in
:numref:`Fig. %s <fig-hprwheel>`.

.. _fig-hprwheel:

.. figure:: plots/hpr-wheel.*
   :width: 10.00000cm

   Helical wheel projection of the N-terminal helix of HPr.