Summary
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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Yang, W., Lee, HW., Pu, M., Hellinga, H., Yang, J.J. (2002). Identifying and Designing of Calcium Binding Sites in Proteins by Computational Algorithm. In: Dadmun, M.D., Van Hook, W.A., Noid, D.W., Melnichenko, Y.B., Sumpter, B.G. (eds) Computational Studies, Nanotechnology, and Solution Thermodynamics of Polymer Systems. Springer, Boston, MA. https://doi.org/10.1007/0-306-47110-8_12
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DOI: https://doi.org/10.1007/0-306-47110-8_12
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