Protein-related items#
To analyze the secondary structure of a protein (not only for static
structures, but also for trajectories), you can use the program
gmx dssp, which is a native implementation of DSSP
algorithm 176, but also is based on the (DSSP
V.4 algorithm) 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
To evaluate this Ramachandran plot you can use the program gmx rama. A typical output is given in Fig. 61.
When studying