A comparison of techniques for calculating protein essential dynamics Export

@article{citeulike:4210865, 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-\&agr; 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 \&phgr;/\&psgr; torsion angle space is discussed. {\copyright} 1997 by John Wiley \& Sons, Inc.}, address = {Department of Biochemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; Groningen Biomolecular Sciences and Biotechnology Institut (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands}, author = {Van Aalten, D. M. F. and de Groot, Bert L. and Findlay, J. B. C. and Berendsen, H. J. C. and Amadei, A.}, citeulike-article-id = {4210865}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/(SICI)1096-987X(19970130)18:2%3C169::AID-JCC3%3E3.0.CO;2-T}, citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/48464/ABSTRACT}, doi = {10.1002/(SICI)1096-987X(19970130)18:2%3C169::AID-JCC3%3E3.0.CO;2-T}, journal = {Journal of Computational Chemistry}, keywords = {articulo, dpca, pca}, number = {2}, pages = {169--181}, posted-at = {2009-03-23 17:37:59}, priority = {0}, title = {A comparison of techniques for calculating protein essential dynamics}, url = {http://dx.doi.org/10.1002/(SICI)1096-987X(19970130)18:2%3C169::AID-JCC3%3E3.0.CO;2-T}, volume = {18}, year = {1997} }

TY - JOUR ID - citeulike:4210865 L3 - citeulike-article-id:4210865 N2 - 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-&agr; 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 &phgr;/&psgr; torsion angle space is discussed. © 1997 by John Wiley & Sons, Inc. IS - 2 JF - Journal of Computational Chemistry AD - Department of Biochemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; Groningen Biomolecular Sciences and Biotechnology Institut (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands EP - 181 TI - A comparison of techniques for calculating protein essential dynamics VL - 18 SP - 169 KW - articulo KW - dpca KW - pca AU - Van Aalten, DMF AU - de Groot, Bert AU - Findlay, JBC AU - Berendsen, HJC AU - Amadei, A PY - 1997/// UR - http://dx.doi.org/10.1002/(SICI)1096-987X(19970130)18:2%3C169::AID-JCC3%3E3.0.CO;2-T ER -