Two web-interfaces to 3DNA, and more

As a nice surprise, I found in the 2009 web-server issue of NAR published on July 1, two articles on web-interface to 3DNA back-to-back:

1. "3D-DART: a DNA structure modelling server" by van Dijk and Bonvin from Utrecht University, The Netherlands. Excerpt from the abstract:

   As a response to the demand for 3D-structural models reflecting the intrinsic plasticity of DNA we present the 3D-DART server (3DNA-Driven DNA Analysis and Rebuilding Tool). The server provides an easy interface to a powerful collection of tools for the generation of DNA-structural models in custom conformations. The computational engine beyond the server makes use of the 3DNA software suite together with a collection of home-written python scripts.

2. "Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures" by Zheng, me and Olson. Excerpt from the abstract:

   The w3DNA (web 3DNA) server is a user-friendly web-based interface to the 3DNA suite of programs for the analysis, reconstruction, and visualization of three-dimensional (3D) nucleic-acid-containing structures, including their complexes with proteins and other ligands.

While I was aware of 3D-DART prior to its publication, I certainly did not expect it to appear in the same issue as w3DNA of which I am a co-author. There is nothing more compelling to illustrate 3DNA's value to the community than a third-party web-interface to it! Combined together, these two web-servers make 3DNA much more accessible to even wider audience. Specifically, they could well serve for education purposes, e.g., to conveniently build a DNA-model of A-, B- or C-form, with user-supplied sequences. Users would be glad to have a choice that better fits their needs. In the long run, the one which provides best user-support will survive.

It is also worthy noting the in the same 2009 NAR web-server issue, another paper titled "SARA: a server for function annotation of RNA structures" by Capriotti and Marti-Renom from Spain also makes use of 3DNA. This serves to emphasize the point that 3DNA is not just for DNA, but for RNA as well -- 3DNA has unique features for RNA that are not found in other currently available software tools that I am aware of.