Journal archive > 2004 > N2, March-April

Generalized ordering parameter S2 as measure of the conformational
flexibility of proteins: comparison of algorithms of S2 calculation
from molecular dynamics simulation data

D. B. KovalskyyO. S. Ivanova, V. M. Dubyna, D. S. Kanibolotsky, O. I. Kornelyuk

NMR spectroscopy in combination with molecular dynamics (MD) simulation technique is a powerful tool for investigation of biomolecule conformations. In the present study we compare the two algorithms of calculation of the generalized order parameter S2 for the peptide N-H bond from MD simulation data. The program based on this algorithm has been written and the effect of an adjustible parameter on results of calculation was studied. HIV–1 protease MD simulation was performed during 7.36 ns using GROMACS 3.1.4. software package. The calculated order parameter values are in good agreement with those obtained by other authors using NMR.

Recieved: 2003-10-10

Published at the site: 2004-04-04

 

The original article in Russian is available for download in PDF format.