An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data

BACKGROUND: Superpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, some atoms are missing from their original structures. Current superposition implementations address the missing data crudely by ignoring such atoms from their structures. RESULTS: In this paper, we propose an effective method for superpositioning pairwise and multiple structures without sequence alignment. It is a two-stage procedure including data reduction and data registration. CONCLUSIONS: Numerical experiments demonstrated that our method is effective and efficient. The code package of protein structure superposition method for addressing the cases with missing data is implemented by MATLAB, and it is freely available from: http://sourceforge.net/projects/pssm123/files/?source=navbar ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13015-016-0079-3) contains supplementary material, which is available to authorized users.