We also show that MICAN program is the fastest non-sequential structure alignment program among all the programs we examined here. Further, although MICAN does not specialize in sequential structure alignment, it showed the top level performance on the sequential test sets. We show that MICAN outperforms the other existing methods for reproducing reference alignments of non-sequential test sets. We compared MICAN with other 9 publicly available structure alignment programs, using both reference-dependent and reference-independent evaluation methods on a variety of benchmark test sets which include both sequential and non-sequential alignments. One of the key feature of the algorithm is utilizing the multiple vector representation for each SSE, which enables us to correctly treat bent or twisted nature of long SSE. The algorithm was designed so as to identify the best structural alignment between protein pairs by disregarding the connectivity between secondary structure elements (SSE). We have developed a novel protein structure alignment algorithm, MICAN (a structure alignment algorithm that can handle M ultiple-chain complexes, I nverse direction of secondary structures, C α only models, A lternative alignments, and N on-sequential alignments). For this purpose, highly accurate sequence order independent structure comparison methods are needed. 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. 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.
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