Create DSSP and HSSP files
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Coos Baakman
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README.md

The source code for building the mkdssp, mkhssp, hsspconv, and hsspsoap programs is bundled in the xssp project. The DSSP executable is mkdssp.

Development

The provided Dockerfile sets up a development environment. Build the docker image using the command docker build -t xssp . and run the image in a container, with a local source copy and data files mounted, with the command docker run -v /home/jon/projects/xssp:/app -v /mnt/extra:/srv/data -it xssp.

Download and installation instructions

Pre-compiled old versions of DSSP are available from the old repository. New source code archives are available here.

Compiling xssp programs

Pre-requisites

System libraries:

  • libzeep version >= 3.0
  • libboost version >= 1.48
  • libbz2
  • autoconf
  • automake
  • autotools-dev

Instructions

Download and uncompress the xssp source code archive (version >= 2.2.6):

wget https://github.com/cmbi/xssp/archive/xssp-2.?.?.tar.gz
tar -zxvf xssp-2.?.?.tar.gz
cd xssp-2.?.?.tar.gz

Configure and build the xssp executables:

./autogen.sh
./configure
make

To build only one executable of the xssp project, e.g. mkdssp, type:

make mkdssp

To test the mkdssp executable type:

./mkdssp

To add the executables to /usr/local/bin type:

sudo make install

Citing xssp

The reference for the new versions of xssp and other protein structure bioinformatics facilities is:

A series of PDB-related databanks for everyday needs
Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek,
 E. Krieger, Robbie P. Joosten and Gert Vriend.
Nucl. Acids Res. (2015) 43, D364-D368

The original reference for DSSP is:

Dictionary of protein secondary structure: pattern recognition of
 hydrogen-bonded and geometrical features.
Kabsch W and Sander C, Biopolymers (1983) 22, 2577-2637.

The original reference for HSSP is:

Database of homology-derived protein structures and the structural
 meaning of sequence alignment.
Sander C and Schneider R, Proteins (1991) 9, 56-68.

Contact

In 2013, maintenance of xssp has been taken over from Maarten Hekkelman by Coos Baakman, Jon Black, and Wouter Touw. If you want to provide feedback, either send an e-mail to xssp.cmbi@radboudumc.nl or have a look at existing issues (if necessary, create a new issue).