A comparison of techniques for calculating protein essential dynamics
Article first published online: 7 DEC 1998
Copyright © 1997 John Wiley & Sons, Inc.
Journal of Computational Chemistry
Volume 18, Issue 2, pages 169–181, 30 January 1997
How to Cite
Van Aalten, D. M. F., De Groot, B. L., Findlay, J. B. C., Berendsen, H. J. C. and Amadei, A. (1997), A comparison of techniques for calculating protein essential dynamics. J. Comput. Chem., 18: 169–181. doi: 10.1002/(SICI)1096-987X(19970130)18:2<169::AID-JCC3>3.0.CO;2-T
- Issue published online: 7 DEC 1998
- Article first published online: 7 DEC 1998
- Manuscript Accepted: 3 MAY 1996
- Manuscript Received: 20 JUN 1995
Recently the basic theory of essential dynamics, a method for extracting large concerted motions from protein molecular dynamics trajectories, was described. Here, we introduce and test new aspects. A method for diagonalizing large covariance matrices is presented. We show that it is possible to perform essential dynamics using different subsets of atoms and compare these to the basic C-α analysis. Essential dynamics analyses are also compared to the normal modes method. The stability of the essential space during a simulation is investigated by comparing the two halves of a trajectory. Apart from the analyses in Cartesian space, the essential dynamics in ϕ/ψ torsion angle space is discussed. © 1997 by John Wiley & Sons, Inc.