Ernesto Estrada1. 1. Faculty of Pharmacy, Department of Organic Chemistry, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain. estrada66@yahoo.com
Abstract
MOTIVATION: The characterization of the folding degree of chains is central to the elucidation of structure--function relationships in proteins. Here we present a new index for characterizing the folding degree of a (protein) chain. This index shows a range of features that are desirable for the study of the relation between structure and function in proteins. RESULTS: A novel index characterizing the folding degree of (protein) chains is developed based on the spectral moments of a matrix representing the dihedral angles (phi, omega and epsilon) of the protein main chain. The proposed index is normalized to the chain size, is not correlated to the gyration radius of the backbone chain and is able to distinguish between structures for which the sum of the main-chain dihedral angles is identical. The index is well correlated to the percentages of helix and strand in proteins, shows a linear dependence with temperature changes, and is able to differentiate among protein families. AVAILABILITY: On request from the author.
MOTIVATION: The characterization of the folding degree of chains is central to the elucidation of structure--function relationships in proteins. Here we present a new index for characterizing the folding degree of a (protein) chain. This index shows a range of features that are desirable for the study of the relation between structure and function in proteins. RESULTS: A novel index characterizing the folding degree of (protein) chains is developed based on the spectral moments of a matrix representing the dihedral angles (phi, omega and epsilon) of the protein main chain. The proposed index is normalized to the chain size, is not correlated to the gyration radius of the backbone chain and is able to distinguish between structures for which the sum of the main-chain dihedral angles is identical. The index is well correlated to the percentages of helix and strand in proteins, shows a linear dependence with temperature changes, and is able to differentiate among protein families. AVAILABILITY: On request from the author.
Authors: Georgios A Pavlopoulos; Maria Secrier; Charalampos N Moschopoulos; Theodoros G Soldatos; Sophia Kossida; Jan Aerts; Reinhard Schneider; Pantelis G Bagos Journal: BioData Min Date: 2011-04-28 Impact factor: 2.522
Authors: Andreas Dander; Laurin Aj Mueller; Ralf Gallasch; Stephan Pabinger; Frank Emmert-Streib; Armin Graber; Matthias Dehmer Journal: Source Code Biol Med Date: 2013-11-13