Our studies for the identification of the natural calcium binding sites with both classic and pseudo EF-hand motifs in three EF-hand proteins have shown that natural calcium binding sites can be accurately relocated with Dezymer using a set of geometric descriptions of an ideal pentagonal bipyramid. The success of each constructed site can be ranked by the relative U(p) values. The searched native-like sites in three EF-hand proteins have the smallest deviation from the target geometry. Our work indicates that a useful method for searching calcium-binding sites in proteins has been established. It is possible to use established parameters to design novel calcium binding proteins.

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