DSSP¶
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.
Install the DSSP package
sudo apt-get install dssp
The program installs itself as
mkdssp
, notdssp
, and Biopython looks to executedssp
, so we need to symlink the namedssp
tomkdssp
sudo ln -s /usr/bin/mkdssp /usr/bin/dssp
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.
all_dssp_props
(filename, file_type)[source]¶ Returns a large dictionary of SASA, secondary structure composition, and surface/buried composition. Values are computed using DSSP. Input: PDB or MMCIF filename Output: Dictionary of values obtained from dssp
-
ssbio.protein.structure.properties.dssp.
calc_sasa
(dssp_df)[source]¶ Calculation of SASA utilizing the DSSP program.
DSSP must be installed for biopython to properly call it. Install using apt-get on Ubuntu or from: http://swift.cmbi.ru.nl/gv/dssp/
Input: PDB or CIF structure file Output: SASA (integer) of structure
-
ssbio.protein.structure.properties.dssp.
calc_surface_buried
(dssp_df)[source]¶ Calculates the percent of residues that are in the surface or buried, as well as if they are polar or nonpolar. Returns a dictionary of this.
-
ssbio.protein.structure.properties.dssp.
get_dssp_df_on_file
(pdb_file, outfile=None, outdir=None, outext='_dssp.df', force_rerun=False)[source]¶ Run DSSP directly on a structure file with the Biopython method Bio.PDB.DSSP.dssp_dict_from_pdb_file
Avoids errors like: PDBException: Structure/DSSP mismatch at <Residue MSE het= resseq=19 icode= > by not matching information to the structure file (DSSP fills in the ID “X” for unknown residues)
Parameters: - pdb_file – Path to PDB file
- outfile – Name of output file
- outdir – Path to output directory
- outext – Extension of output file
- force_rerun – If DSSP should be rerun if the outfile exists
Returns: DSSP results summarized
Return type: DataFrame