Title: Algorithms to compare pentagonal pyramidal/bipyramidal metal complexes on protein structure

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: The task of identifying the inherent features of a coordination complex by comparing two such complexes is not trivial, as such complexes may have different geometries. For obtaining deviation statistics due to such comparisons in which the function of one complex is known and the other is unknown based on the protein's structure, in this study one algorithm has been proposed that is capable of comparing two complexes in which a pair of structures possesses pentagonal pyramidal/bipyramidal geometries. The proposed algorithm applies some mathematical transformations to both of the comparing structures so that minimum mean square error (MSE) will be produced due to their deviations and produces various statistical reports that will be beneficial for researchers from different fields of studies. To evaluate the performance of the proposed model, a total of 38 pentagonal pyramidal calcium binding sites and 254 pentagonal bipyramidal calcium and iron binding sites on protein's structure have been tested.

Keywords: algorithms for bioinformatics; coordination complex; shape of coordination complex; metalloprotein; VSEPR theory.

DOI: 10.1504/IJCBDD.2024.142266

International Journal of Computational Biology and Drug Design, 2024 Vol.16 No.2, pp.112 - 124

Accepted: 08 Jun 2024
Published online: 16 Oct 2024 *

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