Premium
A comparison of techniques for calculating protein essential dynamics
Author(s) -
Van Aalten D. M. F.,
De Groot B. L.,
Findlay J. B. C.,
Berendsen H. J. C.,
Amadei A.
Publication year - 1997
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(19970130)18:2<169::aid-jcc3>3.0.co;2-t
Subject(s) - molecular dynamics , cartesian coordinate system , dynamics (music) , statistical physics , space (punctuation) , covariance , stability (learning theory) , computer science , trajectory , physics , mathematics , geometry , quantum mechanics , statistics , acoustics , machine learning , operating system
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.