mkdssp(1) USER COMMANDS mkdssp(1)
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 appli-
cation 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 iden-
tifier.
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 col-
umn 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 nega-
tive).
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 Angstrom 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 col-
umn 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 improve-
ment would be to use angle dependent H-bond energy calculation.
BUGS
If you find any, please let me know.
AUTHOR
Maarten L. Hekkelman (m.hekkelman (at) cmbi.ru.nl)
version 2.0.4 18-apr-2012 mkdssp(1)