The DSSP database

The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).

Information

• The help document for the DSSP program.
• The license form for an academic DSSP source code.
• The license form for a commercial DSSP source code.
• A bill for commercial users.
• AFTER faxing the license form to the FAX number indicated at the form (+31 (0)24 3652977) you can extract the DSSP distribution by clicking here or from the anonymous FTP area of ftp.cmbi.kun.nl. Do a cd to pub/molbio/software and download DsspCMBI.tar.gz . In any case, type tar -xvzf DsspCMBI.tar.gz to unpack, then look at README.TXT.
• Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp >messages.txt
• Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code.
• Commercial users are requested to transfer Euro 1000 to account number of the "Stichting WHAT IF" no. 54.83.62.262 at the ABN-AMRO in Nijmegen. Please mention DSSP. Please transfer the money before down-loading the software.
• We have available (warning, that is 23 MEGA bytes) a version of the PDBFINDER with the secondary structure according to DSSP indicated as 1-letter code strings. Look at the example.
• FTP access to the database files at the EMBL (many files).
• Secondary structure and a bit more but in a different format. (There is some help for this format).

'News'

In 1994, a fast algorithm for surface calculation was added to the accessibility module.
The July-1995 version has a slightly changed output format. and several runtime options under unix. Over the years many people have contributed to the maintenance of DSSP. Most noticebly Michael Scharf and Rob Hooft. In 2000 maintenance was taken over by Elmar Krieger.

Reference

The DSSP code

• H = alpha helix
• B = residue in isolated beta-bridge
• E = extended strand, participates in beta ladder
• G = 3-helix (3/10 helix)
• I = 5 helix (pi helix)
• T = hydrogen bonded turn
• S = bend

Problems?