Why MSSP has two options for Multiple Structures Alignment Software?

MSSP allows users to choose between two Multiple Structures Alignment (MSA) programs: MUSTANG[1] and MAMMOTH-mult[2]. Although both programs implement horizontal-first methods (pairwise alignments are progressively merged into an MSA), one must bear in mind that results can differ significantly. In order to illustrate that, we compare MSSP outputs from MUSTANG (Fig. 1) and MAMMOTH-mult (Fig. 2) by using a set of seven dihydrofolate reductases[3], all bellonging to SCOP family c.71.1.1 (4dfr:A, 1ra8:A, 5dfr:A, 1dhf:A, 1mvs:A, 1ia1:B and 1ia3:A).

Gray marked background on sequence alignments indicate area of some significant differences in MUSTANG vs MAMMOTH-mult output. The consequence of those differences are the differences shown also on the MSSP 2D plot. Such approach might help in deciphering some extra details about structure-function relationship that would otherwise stay hidden. In other words, a bit different structural alignment might give an additional insight into STING's descriptors of the same loci at the MSA.

References

  1. Konagurthu, A. S., Whisstock, J. C., Stuckey, P. J., & Lesk, A. M. (2006). MUSTANG: a multiple structural alignment algorithm. Proteins: Structure, Function, and Bioinformatics, 64(3), 559-574.
  2. Lupyan, D., Leo-Macias, A., & Ortiz, A. R. (2005). A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics, 21(15), 3255-3263.
  3. Krissinel, E., & Henrick, K. (2005). Multiple alignment of protein structures in three dimensions. In Computational Life Sciences (pp. 67-78). Springer Berlin Heidelberg.