In the September 6, 2011 issue of PNAS (vol. 108, no. 36), AlQuraishi and McAdamsa from Stanford University published a high-profile article "Direct inference of protein–DNA interactions using compressed sensing methods" (pp. 14819–14824). See also the thoughtful Commentary by Vijay Pande, "(Compressed) sensing and sensibility". Essentially, by combining concepts from compressed sensing and statistical mechanics, AlQuraishi and McAdamsa have developed a novel approach to determine the energy potential of protein–DNA complexes, leading to "an impressive advance in predictive capability" -- ~90% accuracy compared with ~60% for the best-performing alternative computational methods.
I am so glad to find that 3DNA (ref nos. 12 and 13) was used in the work:
In silico mutagenesis was carried out using the 3DNA software package (12, 13), which maintains the backbone atoms of the DNA molecule, but replaces the base pair atoms in a way that is consistent with the backbone orientation in the crystal. (p.14821, middle of the right column)
Hopefully, the new and novel base mutation functionality in 3DNA will find more applications and be in wider use. Surely, I'll respond promptly to users' feedback and refine related 3DNA tools as necessary.