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:
|B or b||Isolated bridge|
|C||Coil (none of the above)|
Installation instructions (Unix)¶
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
In the shell¶
To run the program on its own in the shell…
To run the program using the ssbio Python wrapper, see:
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!