mkdssp - Online in the Cloud

PROGRAM:

NAME

mkdssp - Calculate secondary structure for proteins in a PDB file

SYNOPSIS

mkdssp [OPTION] pdbfile [dsspfile]

DESCRIPTION

The mkdssp program was originally designed by Wolfgang Kabsch and Chris Sander to
standardize secondary structure assignment. DSSP is a database of secondary structure
assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and
mkdssp is the application that calculates the DSSP entries from PDB entries. Please note
that mkdssp does not predict secondary structure.

OPTIONS

If you invoke mkdssp with only one parameter, it will be interpreted as the PDB file to
process and output will be sent to stdout. If a second parameter is specified this is
interpreted as the name of the DSSP file to create. Both the input and the output file
names may have either .gz or .bz2 as extension resulting in the proper compression.

-i, --input filename
The file name of a PDB formatted file containing the protein structure data. This
file may be a file compressed by gzip or bzip2.

-o, --output filename
The file name of a DSSP file to create. If the filename ends in .gz or .bz2 a
compressed file is created.

-v, --verbose
Write out diagnositic information.

--version
Print the version number and exit.

-h, --help
Print the help message and exit. The directory containing the parser scripts for
mrs.

THEORY

The DSSP program works by calculating the most likely secondary structure assignment given
the 3D structure of a protein. It does this by reading the position of the atoms in a
protein (the ATOM records in a PDB file) 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.

This means you do need to have a full and valid 3D structure for a protein to be able to
calculate the secondary structure. There's no magic in DSSP, so e.g. it cannot guess the
secondary structure for a mutated protein for which you don't have the 3D structure.

DSSP FILE FORMAT

The header part of each DSSP file is self explaining, it contains some of the information
copied over from the PDB file and there are some statistics gathered while calculating the
secondary structure.

The second half of the file contains the calculated secondary structure information per
residue. What follows is a brief explanation for each column.

Column Name Description
───────────────────────────────────────────────────────────────────────────────────────────
# The residue number as counted by mkdssp
RESIDUE The residue number as specified by the PDB file
followed by a chain identifier.

AA The one letter code for the amino acid. If this
letter is lower case this means this is a
cysteine that form a sulfur bridge with the
other amino acid in this column with the same
lower case letter.
STRUCTURE This is a complex column containing multiple sub
columns. The first column contains a letter
indicating the secondary structure assigned to
this residue. Valid values are:
Code Description
H Alpha Helix
B Beta Bridge
E Strand
G Helix-3
I Helix-5
T Turn
S Bend
What follows are three column indicating for
each of the three helix types (3, 4 and 5)
whether this residue is a candidate in forming
this helix. A > character indicates it starts a
helix, a number indicates it is inside such a
helix and a < character means it ends the helix.
The next column contains a S character if this
residue is a possible bend.
Then there's a column indicating the chirality
and this can either be positive or negative
(i.e. the alpha torsion is either positive or
negative).
The last two columns contain beta bridge labels.
Lower case here means parallel bridge and thus
upper case means anti parallel.
BP1 and BP2 The first and second bridge pair candidate, this
is followed by a letter indicating the sheet.
ACC The accessibility of this residue, this is the
surface area expressed in square Ångstrom that
can be accessed by a water molecule.
N-H-->O..O-->H-N Four columns, they give for each residue the
H-bond energy with another residue where the
current residue is either acceptor or donor.
Each column contains two numbers, the first is
an offset from the current residue to the
partner residue in this H-bond (in DSSP
numbering), the second number is the calculated
energy for this H-bond.
TCO The cosine of the angle between C=O of the
current residue and C=O of previous residue. For
alpha-helices, TCO is near +1, for beta-sheets
TCO is near -1. Not used for structure
definition.
Kappa The virtual bond angle (bend angle) defined by
the three C-alpha atoms of the residues current
- 2, current and current + 2. Used to define
bend (structure code 'S').
PHI and PSI IUPAC peptide backbone torsion angles.
X-CA, Y-CA and Z-CA The C-alpha coordinates

HISTORY

The original DSSP application was written by Wolfgang Kabsch and Chris Sander in Pascal.
This version is a complete rewrite in C++ based on the original source code. A few bugs
have been fixed since and the algorithms have been tweaked here and there.

TODO

The code desperately needs an update. The first thing that needs implementing is the
improved recognition of pi-helices. A second improvement would be to use angle dependent
H-bond energy calculation.

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