What's New?

We are maintaining the 3DNA forum for Q&As. Please do take advantage of this forum, instead of sending me emails: this will benefit everyone! Only under very special circumferences will your questions be answered directly by email. Most likely, you will be referred back to the forum.

Periodically (usually on a weekly basis), we update the 3DNA citation list by checking Web of Science. If your publication citing 3DNA is somehow not covered by Web of Science, please drop us a message with citation details so we can make the list as complete as possible. From a personal perspective, following the citations has turned out to be an excellent way to keep myself informed since I am working on the 3DNA project strictly in my spare time. [Last updated: Friday Jul 18, 2008 with 225 citations]

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.

3DNA was created by Dr. Xiang-Jun Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey. Since leaving Rutgers, Dr. Lu has continued to work on this project as an independent consultant in his spare time. This updated website provides users with more background information and technical details about 3DNA, including working examples. Thus, those who are really interested in nucleic acid structures can have a clear understanding of "what's going on in that black box".

3DNA has benefited greatly from interactions with the Nucleic Acid Database (NDB) project led by Professor Helen Berman. Dr. Zukang Feng at the PDB/NDB, Dr. A. R. Srinivarsan, Ms. Yurong Xin, Mr. Andrew Colasanti, Mr. Jin Tao, Ms. Fei Xu and other members of the Olson lab., and numerous users from around the globe have helped in making 3DNA a better tool to serve the scientific community.

This site has been tested to work on Windows 2000/XP running IE v5.0/6.0 and NetScape 7.2, RedHat Linux running Mozilla v1.4, and Mac OS X running IE v5.1 and Safari. It does not work on SGI running NetScape v4.7. Please let us know if have any problem with other OS/browser combinations.