A COMPARISON OF TECHNIQUES FOR CALCULATING PROTEIN ESSENTIAL DYNAMICS

Recently the basic theory of essential dynamics, a method for extracti ng large concerted motions from protein molecular dynamics trajectorie s, was described. Here, we introduce and test new aspects. A method fo r diagonalizing large covariance matrices is presented. We show that i t is possible to perform essential dynamics using different subsets of atoms and compare these to the basic C-or analysis. Essential dynamic s analyses are also compared to the normal modes method. The stability of the essential space during a simulation is investigated by compari ng the two halves of a trajectory. Apart from the analyses in Cartesia n space, the essential dynamics in phi/psi torsion angle space is disc ussed. (C) 1997 by John Wiley & Sons, Inc.