A comparison of techniques for calculating protein essential dynamics

✍ Scribed by Van Aalten, D. M. F.; De Groot, B. L.; Findlay, J. B. C.; Berendsen, H. J. C.; Amadei, A.

• Publisher: John Wiley and Sons
• Year: 1997
• Tongue: English
• Weight: 443 KB
• Volume: 18
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/(sici)1096-987x(19970130)18:2<169::aid-jcc3>3.0.co;2-t

✦ Synopsis

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-␣ 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 r torsion angle space is discussed.