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DSSP

DSSP calculations

Description

DSSP (Define Secondary Structure of Proteins) is the standard method used to assign secondary structure annotations to a protein structure. DSSP utilizes the atomic coordinates of a structure to assign the secondary codes, which are:

Code Description
H Alpha helix
B Beta bridge
E Strand
G Helix-3
I Helix-5
T Turn
S Bend

Furthermore, DSSP calculates geometric properties such as the phi and psi angles between residues and solvent accessibilities. ssbio provides wrappers around the Biopython DSSP module to execute and parse DSSP results, as well as converting the information into a Pandas DataFrame format with calculated relative solvent accessbilities (see ssbio.protein.structure.properties.dssp for details).

Installation instructions (Ubuntu)

Note

These instructions were created on an Ubuntu 17.04 system.

  1. Install the DSSP package

    sudo apt-get install dssp

  2. The program installs itself as mkdssp, not dssp, and Biopython looks to execute dssp, so we need to symlink the name dssp to mkdssp

    sudo ln -s /usr/bin/mkdssp /usr/bin/dssp
  3. Then you should be able to run dssp in your terminal

Installation instructions (Mac OSX)

Program execution

In the shell

To run the program on its own in the shell...

dssp -i <path_to_pdb_file> -o <new_path_to_output_file>

With ssbio

To run the program using the ssbio Python wrapper, see: ssbio.protein.structure.properties.dssp.get_dssp_df_on_file

FAQs

  • How do I cite DSSP?

    • Kabsch W & Sander C (1983) DSSP: definition of secondary structure of proteins given a set of 3D coordinates. Biopolymers 22: 2577–2637

  • I'm having issues running DSSP...

    • See the ssbio wiki for (hopefully) some solutions - or add yours in when you find the answer!

API

ssbio.protein.structure.properties.dssp