3DNA Nature Protocols Paper [vol.3, no.7 (2008), 1213-1227]

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As you may already know, a new paper on 3DNA was published in the July 3, 2008 issue of Nature Protocols (NP). Even though this publication has been referred to a few times in the forum, especially in the post by Tomas, I have recently been too busy to  make a formal announcement here. Now, I feel it is the time to get the message out.

First of all, we appreciate your contributions:

We are grateful ... to the users of 3DNA for using the software to address real-world problems, and communicating the difficulties that they encounter. Positive interactions with the users have been the driving force behind the development and improvement of 3DNA.

Following the editor's suggestion, I would encourage you to post your comments and questions related to the protocols paper in the NP website: it is a more prominent and permanent place than the 3DNA forum. You are welcome, of course, to post any 3DNA-related questions in this forum.

In this paper, I selected seven representative examples to illustrate the versatile capabilities made possible only by 3DNA's integrated approach that combines structural analysis, rebuilding and visualization (see the composite image below). Hopefully, I have convinced you that 3DNA is not just for DNA as suggested on the nuccyl website (see also http://xiang-jun.blogspot.com/2009/07/does-3dna-work-for-rna.html), or only for structural analysis (as Curves etc). Importantly, in the NP_Recipes subdirectory distributed with 3DNA v2.0,  I have included all scripts, original data files and generated images, so that qualified researchers should be able to reproduce accurately our results without difficulty. Of course, I am more than willing and would be quick to address any reproducibility issues you may have. Repeatability is one of the basic requirements of a published scientific work, yet in this "high-throughput" / "big science" age reproducibility is sort of becoming a luxury.

Over the years, it has also become quite clear to me that 3DNA is still (heavily) underused, especially with regard to its visualization capabilities, and analysis functionality for RNA structures. Moreover, and most importantly, 3DNA can be refined, extended, and tailored to new applications. I am especially interested in forging serious collaborations with those having real insights in structural biology, willing to share and being responsive: with complementary expertises, some mutual interests and a commitment to excellence, we can have fun together in solving challenging problems in biological (especially RNA) structures.

Xiang-Jun Lu

Cleaned up links on 2012-02-28