Calculating Secondary Structure Superposition

The secondary structure superposition calculation is the method offered through the Spruce TK to superimpose two structures using the shape of their secondary structure elements. This example shows how to calculate such a structural superposition.

Command Line Interface

This simple example takes in a reference and a fit protein, and aligns their secondary structure elements using a shape-based method.

prompt> secondarystructuresuperposition <reference protein> <fit protein>

Code

Download code

secondarystructuresuperposition.py and both 1A29.pdb (the reference PDB file) and 1CLL.pdb (the fit PDB file)

Example

prompt> secondarystructuresuperposition.py 1A29.pdb 1CLL.pdb

will generate the following output:

Tanimoto score for the secondary structure fit of 1CLL.pdb to 1A29.pdb is 0.305181 (arb. units).

Writing superimposed fit protein to 1CLL_sp.oeb.gz