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mkdssp

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.

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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.

BUGS

If you find any, please let me know.

AUTHOR

Maarten L. Hekkelman (m.hekkelman (at) cmbi.ru.nl)

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