A Comparative Study of Methodologies of Protein Secondary Structure - Computational Intelligence Techniques for Comparative Genomics - page 38

Fig. 2 a Represents the antiparallel beta sheet and b represents the parallel beta sheets

3.1 The DSSP

DSSP stands for dictionary of secondary structures. We generally take a non-
homologous protein structure to calculate the protein structure. DSSP is a program
that is used to convert or transfer the number of states that is it is used to decrease
the number of states of residues from eight to three [ 3 ]. The reason behind the
decrease of the number of states is to predict the secondary structure that consists of
ʱ rst designed by Wolfgang Kabsch and

Chris Sander to standardize the secondary structure assignment. DSSP is a database
of secondary structure assignments for all protein entries in the protein data bank
(PDB).
Brief history: The original DSSP application was written between 1983 and
1988 in the programming language PASCAL. This PASCAL code is automatically
converted but maintaining this proved to be a lot of trouble-taking.
Working: The DSSP program works by calculating the most likely secondary
structure assignment that was given in the 3D structure of a protein [ 2 ]. It does this
by reading the position of the atoms in a protein followed by calculation of the H-
bond energy between all atoms. The best two H-bonds for each atom are then used
to determine the most likely class of secondary structure for each residue in the
protein.
Structure: The structure of the DSSP is as follows:

helices, ʲ -sheet, coil, and fold. It was

G = 3-turn helix (3 10 helix). Min length 3 residues.
H = 4-turn helix ( ʱ helix). Min length 4 residues.

helix). Min length 5 residues.
T = hydrogen bonded turn (3, 4, or 5 turn)

I = 5-turn helix ( ˀ