This repo is outdated. Please go to https://github.com/PDB-REDO/dssp
The provided Dockerfile sets up a development environment. Build the docker
image using the command docker build -t dssp . 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/dssp:/app -v /mnt/extra:/srv/data -it dssp.
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:
- libboost version >= 1.48
- libz
- libbz2
- autoconf
- automake
- autotools-dev
This requires docker >= 1.12.3 and docker-compose >= 1.8.1.
From the repository, run:
docker-compose build
Then, to run mkdssp:
docker-compose run dssp ./mkdssp
From inside this repository, configure and build the dssp executables:
./autogen.sh
./configure
make
To build only one executable of the dssp 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 dssp 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 dssp 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 dssp.cmbi@radboudumc.nl or have a look at existing issues (if necessary, create a new issue).