On novel representation of proteins based on amino acid adjacency matrix

Abstract

A novel characterization of proteins is presented based on selected properties of recently introduced 20 × 20 amino acid adjacency matrix of proteins in which matrix elements count the occurrence of all 400 possible pair-wise adjacencies obtained by reading protein primary sequence from the left to the right. In particular we consider the characterization based on the sum and the difference of the rows and the corresponding columns, which characterize proteins by a pair of 20-component vectors. The approach is illustrated on a set of ND6 proteins of eight species.

^†Visitor, Emeritus, Department of Mathematics and Computer Science, Drake University, Des Moines, IA, USA.

Keywords:

• amino acid adjacency matrix
• graphical representation of proteins
• ND6 proteins
• 20-component vectors

Acknowledgments

The authors thank the Slovenian Ministry of Higher Education, Science and Technology for financial support under contracts P1-017 and No. 1000-07-780003.

Notes

^†Visitor, Emeritus, Department of Mathematics and Computer Science, Drake University, Des Moines, IA, USA.