Statistical investigation of surface bound ions and further development of BION server to include pH and salt dependence |
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| Authors: | Marharyta Petukh Min Zhang Emil Alexov |
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| Affiliation: | Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC |
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| Abstract: | Ions are engaged in multiple biological processes in cells. By binding to the macromolecules or being mobile in the solvent, they maintain the integrity of the structure of macromolecules; participate in their enzymatic activity; or screen electrostatic interactions. While experimental methods are not always able to assign the exact location of ions, computational methods are in demand. Although the majority of computational methods are successful in predicting the position of ions buried inside macromolecules, they are less effective in deciphering positions of surface bound ions. Here, we propose the new BION algorithm ( http://compbio.clemson.edu/bion_server_ph/ ) that predicts the location of the surface bound ions. It is more efficient and accurate compared to the previous version since it uses more advanced clustering algorithm in combination with pairing rules. In addition, the BION webserver allows specifying the pH and the salt concentration in predicting ions positions. © 2015 Wiley Periodicals, Inc. |
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| Keywords: | DelPhi electrostatics surface bound ion Poisson– Boltzmann equation clustering |
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