Title: A geometry based approach to compare five metal binding sites on biomolecular structures

Authors: Swati Adhikari; Parthajit Roy

Addresses: Department of Computer Science, The University of Burdwan, Golapbag, Purba Bardhaman, West Bengal, 713104, India ' Department of Computer Science, The University of Burdwan, Golapbag, Purba Bardhaman, West Bengal, 713104, India

Abstract: Characterisation of type or function of a coordination site on the structure of biomolecules - protein, DNA and RNA is a very critical task. Sometimes it is needed to compare a new site with an existing one, to predict structural properties or function of the new site and to compute various coordination statistics. Now, different coordination sites possess different geometries. So, the task is to compare an unknown site with a known one possessing the same geometries and to compute statistics regarding structural deviations. For the same purpose, in this study, three novel algorithms have been proposed that use a geometry-based concept to compare five pairs of coordination sites. To produce minimum mean square error (MSE) due to the structural deviations, some mathematical transformations have been applied on each pair of structures to make them structurally compatible. Bio-researchers get benefitted from the numerous statistical reports obtained with these algorithms.

Keywords: biomolecule-metal interaction; coordination site; coordination number; coordination geometry; VSEPR theory; algorithms in bioinformatics.

DOI: 10.1504/IJCBDD.2022.124751

International Journal of Computational Biology and Drug Design, 2022 Vol.15 No.1, pp.1 - 29

Received: 07 Sep 2021
Accepted: 28 Dec 2021
Published online: 08 Aug 2022 *

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