While updating 3DNA citations this week, I noticed five of them are from the same June 2010 issue of JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (JBSD), which is focused on "Current Perspectives on Nucleosome Positioning". Most of the papers in this issue are from well-known laboratories in computational structural biology. It is my pleasure to see 3DNA being widely used in the important research area of nucleosome positioning.
I browsed through the abstracts of all the papers in this JBSD issue to refresh my knowledge of this field. While DNA sequence surely plays some role in nucleosome positioning, I remain to be convinced of the existence of a nucleosome "code" (yet) in the sense of the generally applicable "genetic code". Overall, DNA is so flexible and the signal is so week, thus allowing for tailored data fitting to specific analysis, which is not transferable to other situations. Clearly, the area is hot, yet still wide open.