3DNA in molecular dynamics simulations

While updating 3DNA citations last Friday, I came across the paper "Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A′-RNA Distinct Conformational Structures?" by Ouyang et al. [Aust. J. Chem. 2009, 62, 1054–1061]. Through molecular dynamics (MD) simulations over a 30 ns period, the authors found that "the identification of distinct A-RNA and A′-RNA structures ... may not be generally relevant in the context of RNA in the aqueous phase." Overall, the paper is nicely written.

I have never performed MD simulations in my research experience, so normally I only read abstracts of such publications just to get a general idea of the main conclusions. What had attracted my attention to this work was its simultaneous citations to three earlier papers:

• Resolving the discrepancies among nucleic acid conformational analyses.


• Overview of nucleic acid analysis programs.


• A standard reference frame for the description of nucleic acid base-pair geometry.

This is quite unusual, since nowadays it is far more common to only cite 3DNA itself (mostly 2003 NAR and/or 2008 NP). So I decided to have a look of the whole paper. It turned out that the authors used the extra citations to justify their choice of using 3DNA instead of Curves to calculate the helical parameters, including "the three main structural descriptors commonly used to differentiate between the two forms of RNA – namely major groove width, inclination and the number of base pairs in a helical twist [turn]".

I communicated to the authors about the availability of Curves+. Specifically, using one case (413D, one of the three structures in their Table 1, "Comparison of different results by CURVES and 3DNA programs"), I've tried to illustrate the point that Curves+ and 3DNA now give directly comparable parameters.

Of course, I am glad to see 3DNA being applied to molecular dynamics simulations of nucleic acid structures. Hopefully, more such applications will show up in the future, and I am willing to offer my help in ways that make sense to me.