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Updated: Apr 17, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
An efficient numerical method for protein sequences similarity analysis based on a new two-dimensional graphical
1a Department of Biophysics, Faculty of Science , Cairo University , Giza , Egypt.
Abstract:
A new two-dimensional graphical representation of protein sequences is introduced. Twenty concentric evenly spaced circles divided by n radial lines into equal divisions are selected to represent any protein sequence of length n. Each circle represents one of the different 20 amino acids, and each radial line represents a single amino acid of the protein sequence. An efficient numerical method based on the graph is proposed to measure the similarity between two protein sequences. To prove the accuracy of our approach, the method is applied to NADH dehydrogenase subunit 5 (ND5) proteins of nine different species and 24 transferrin sequences from vertebrates. High values of correlation coefficient between our results and the results of ClustalW are obtained (approximately perfect correlations). These values are higher than the values obtained in many other related works.
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