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A comparison of techniques for calculating protein essential dynamics
Article first published online: 7 DEC 1998
DOI: 10.1002/(SICI)1096-987X(19970130)18:2<169::AID-JCC3>3.0.CO;2-T
Copyright © 1997 John Wiley & Sons, Inc.
1096-987X/asset/cover.gif?v=1&s=4429aac2462ebd499c13b3d7fe983679c5767778 "Journal of Computational Chemistry")
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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
Publication History
- Issue published online: 7 DEC 1998
- Article first published online: 7 DEC 1998
- Manuscript Accepted: 3 MAY 1996
- Manuscript Received: 20 JUN 1995
- Abstract
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Abstract
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.