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| Research article summary (published 29 Apr 2006): |
Root mean square deviation probability analysis of molecular dynamics trajectories on DNA.
Full Abstract
The comparison and detection of the commonalities and differences in multiple structural ensembles is an important step in the use of molecular simulations to gain insight into the conformation and dynamics of complex biomacromolecules. While the average structure is often employed as the representative of an ensemble of structures in such comparisons, dynamic molecular systems with multiple conformational substates call for a more accurate representation that captures the complete dynamical range of the ensemble. We present a probability analysis procedure based on the root-mean-square differences among the structural ensembles that efficiently and accurately performs the relevant comparison.
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Author information
Author/s: Dixit, Surjit B (SB); Ponomarev, Sergei Y (SY); Beveridge, David L (DL);
Affiliation: Department of Chemistry and Molecular Biophysics Program, Hall-Atwater Laboratories, Wesleyan University, Middletown, Connecticut 06459, USA.
Grants: GM37909 (Agency:NIGMS NIH HHS)
Journal and publication information
Publication Type: Journal Article; Research Support, N.I.H., Extramural
Journal: Journal of chemical information and modeling (J Chem Inf Model), published in United States. (Language: eng)
Reference: -2006 May-Jun; vol 46 (issue 3) : pp 1084-93
Dates: Created 2006/05/22; Completed 2006/06/28; Revised 2007/11/14;
PMID: 16711728, status: MEDLINE (last retrieval date: 12/26/2008)
Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.
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