20D-dynamic representation of protein sequences

Agata Czerniecka; Dorota Bielińska-Wąż; Piotr Wąż; Tim Clark

doi:10.1016/j.ygeno.2015.12.003

20D-dynamic representation of protein sequences

Genomics. 2016 Jan;107(1):16-23. doi: 10.1016/j.ygeno.2015.12.003. Epub 2015 Dec 17.

Authors

Agata Czerniecka¹, Dorota Bielińska-Wąż², Piotr Wąż³, Tim Clark⁴

Affiliations

¹ Department of Radiological Informatics and Statistics, Medical University of Gdańsk, Tuwima 15, 80-210 Gdańsk, Poland.
² Department of Radiological Informatics and Statistics, Medical University of Gdańsk, Tuwima 15, 80-210 Gdańsk, Poland. Electronic address: djwaz@gumed.edu.pl.
³ Department of Nuclear Medicine, Medical University of Gdańsk, Tuwima 15, 80-210 Gdańsk, Poland.
⁴ Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany.

PMID: 26705741
DOI: 10.1016/j.ygeno.2015.12.003

Abstract

A new method of comparison of protein sequences has been formulated. The sequence of amino acids is represented by a set of point masses in a 20D space. The distribution of points in the space is obtained by applying the method of a walk in the 20D space. Projections of the 20D representation into 2D or 3D spaces illustrate the distribution of particular amino acids along the sequence. 20D moments of inertia are proposed as new descriptors of protein sequences.

Keywords: Alignment-free methods; Descriptors; Moments of inertia; Similarity/dissimilarity analysis of protein sequences.

MeSH terms

Algorithms*
Amino Acid Sequence
Molecular Dynamics Simulation*
Protein Conformation
Sequence Analysis, Protein / methods*