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Note

This repo is outdated. Please go to https://github.com/PDB-REDO/dssp

Development

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.

Download and installation instructions

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

Compiling dssp programs

Pre-requisites

Compiler:

  • Must support at least the c++ 11 standard.

System libraries:

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

Instructions to build in Docker

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

Instructions for installing mkdssp locally

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

Citing dssp

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.

Contact

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).