STRIDE¶
Description¶
STRIDE (Structural identification) is a program used to assign secondary structure annotations to a protein structure. STRIDE has slightly more complex criteria to assign codes compared to DSSP. STRIDE utilizes the atomic coordinates of a structure to assign the structure codes, which are:
Code | Description |
---|---|
H | Alpha helix |
G | 3-10 helix |
I | PI-helix |
E | Extended conformation |
B or b | Isolated bridge |
T | Turn |
C | Coil (none of the above) |
Installation instructions (Unix)¶
Note
These instructions were created on an Ubuntu 17.04 system.
Download the source from the STRIDE download page
Create a new folder named “stride” in a place where you store software and extract the source into it
mkdir /path/to/software/stride cp /path/to/downloaded/stride.tar.gz /path/to/software/stride cd /path/to/software/stride tar -zxf stride.tar.gz
Build the program from source and copy its binary:
cd /path/to/software/stride make cp stride /usr/local/bin
Program execution¶
With ssbio¶
To run the program using the ssbio Python wrapper, see: ssbio.protein.path.to.wrapper()
FAQs¶
How do I cite STRIDE?
- Frishman D & Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23: 566–579 Available at: http://dx.doi.org/10.1002/prot.340230412
I’m having issues running STRIDE…
- See the ssbio wiki for (hopefully) some solutions - or add yours in when you find the answer!