MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments
1 Department of Computational Science and Engineering, Nagoya University, Nagoya 464-8603, Japan
2 Department of Applied Physics, Nagoya University, Nagoya 464-8603, Japan
BMC Bioinformatics 2013, 14:24 doi:10.1186/1471-2105-14-24Published: 18 January 2013
Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Further investigation of such protein relationships would give us a hint as to how proteins can change their fold in the course of evolution, as well as a insight into physico-chemical properties of secondary structure packing. For this purpose, highly accurate sequence order independent structure comparison methods are needed.
We have developed a novel protein structure alignment algorithm, MICAN (a structure alignment algorithm that can handle
MICAN is the fastest and the most accurate program among non-sequential alignment programs we examined here. These results suggest that MICAN is a highly effective tool for automatically detecting non-trivial structural relationships of proteins, such as circular permutations and segment-swapping, many of which have been identified manually by human experts so far. The source code of MICAN is freely download-able at http://www.tbp.cse.nagoya-u.ac.jp/MICAN webcite.