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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
![\resizebox{6in}{!}{\includegraphics{lec13_figs/alphamols.ps}}](img16.gif) |
Figure 13.5:
Input Molecules: 1aaj and 1pmy
![\resizebox{6in}{!}{\includegraphics{lec13_figs/mols.ps}}](img18.gif) |
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.
Peer Itsik
2001-03-04