Problem Definition

The input to protein pairwise structural comparison is a set of 3D atomic coordinates of two different molecules (see figure [13.4]).

  

Figure: C coordinates of input molecules

  

Figure 13.5: Input Molecules: 1aaj and 1pmy

The goal is to find a rigid transformation (rotation and translation) in space that matches a ``sufficient'' number of atoms of one molecule to those of the other molecule.
The algorithms that tackle the problem can be divided as follows:

Sequence order dependent

- use the order of atoms on a polypeptyde chain, thus reducing a problem to 3D curve matching, that is essentially a 1D task.