The source code for building the mkdssp, mkhssp, hsspconv, and
hsspsoap programs is bundled in the xssp project. The DSSP executable is
mkdssp.
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.
Pre-compiled old versions of DSSP are available from the old repository. New source code archives are available here.
Compiler:
- Must support at least the c++ 11 standard.
System libraries:
- libzeep version >= 3.0 (for mkhssp --fetch-dbrefs only)
- libboost version >= 1.48
- libbz2
- autoconf
- automake
- autotools-dev
Download and uncompress the xssp source code archive (version >= 2.2.6):
wget https://github.com/cmbi/xssp/archive/xssp-?.?.?.tar.gz
tar -zxvf xssp-?.?.?.tar.gz
cd xssp-?.?.?.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
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.
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).