Background information about 3DNA

3DNA is a versatile package for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures, based on a standard reference frame (Olson et al., J. Mol. Biol. 313(1), 229-237, 2001). In its core, the software uses a simple, yet mathematically rigorous and geometrically sensible, scheme for calculating a complete set of local base-pair, step, and helical parameters, and allows for exact rebuilding of a structure based on these parameters. Unique features of 3DNA include automatic classification of a dinucleotide step as A-, B-, or TA-like based on the positioning of the phosphorus atoms, and the generation of "standardized" base stacking diagrams. The rebuilding routines give Calladine-Drew style schematic representations of DNA as well as full atomic models with the sugar-phosphate backbone.

Since 3DNA v1.5 was released near the end of 2002, many improvements and bug-fixes have been added to the 3DNA software package. Most noticeably, DNAs with B-Z junction can be now be detected and analyzed automatically; 3DNA now also has support for PDBML to generate large nucleic acid structures; the simplified yet more informative block view images, generated by "blocview", have been adopted by both NDB and PDB.

The most significant event in recent years is the publication of the 2008 Nature Protocols paper, entitled "3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures", and the release of 3DNA v2.0. The 3DNA forum has been actively maintained, and any 3DNA-related issues should be communicated there.