Structural alignment

protein structural alignments.

Two protein domain structures can be aligned by superposing their 3D coordinates, with the aim of minimizing the RMSD of the superposition.

Many algorithms have been developed to optimize this complex task.

The task is complex because of the large number of degrees of freedom between two datasets of points in 3D (each molecule has 6 degrees of freedom).

Some approaches use quaternerions to reduce the dimensionality of the space without removing any information (isomorphic translation).