Protein structure provides the opportunity to rec-ognize homology that is undetectable by sequence comparison, and it represents a powerful means of discovering functions, yielding direct insight into the molecular mechanisms. Currently, there are several techniques avail- able in attempting to ?nd the optimal alignment of shared structural motifs between two proteins.In this paper, we show the e?ectiveness of the proposed re?nement methods [11] by a set of ex- periments, which have improved some previous re-sults. We propose a better adaptive strategy to have better parameters, and we can get a better pairwise alignments of protein structures. We can apply this strategy to ?nd more accurate and sim-
ilar protein structure pairings.
