Advantages of the Sequence Independent Alignment

Since the techniques don't exploit chain order, they can detect non-sequential motifs in proteins, such as molecular surface motifs, especially binding sites. In addition, it allows us to search structural databases with only partial structural information. The same algorithms can be applied to other molecular structures, such as drugs. It also provides robustness to insertions and deletions.

Sequence order independent

- align features in 3D space, a real 3D task.