3DNA citations reach over 300

When checking Web of Science today, I found, to my great satisfaction, that citations to the 3DNA 2003 NAR paper have reached over 300. While the number is still not comparable to true classics, it is nevertheless a significant one. It is worth noting that the 300+ citations span 77 scientific journals in the broad biomedical and chemical research fields, including Cell, Nature and Science (well, if CNS really means anything). The top six journals (with over double-digit citations) are:

• 49 -- NUCLEIC ACIDS RESEARCH
• 27 -- JOURNAL OF MOLECULAR BIOLOGY
• 23 -- JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 19 -- BIOCHEMISTRY
  
• 13 -- JOURNAL OF PHYSICAL CHEMISTRY B
• 11 -- BIOPHYSICAL JOURNAL

In retrospect, the wide acceptance of 3DNA by the community is certainly not by chance. Listed below are some of the major factors:

1. 3DNA is built upon the best selected features from a thorough understanding of seven popular DNA structural analysis programs, including Curves, NewHelix/FreeHelix, CEHS, CompDNA, and RNA (Running Nucleic Acids by Babcock and Olson). This is summarized back in June 2003, nearly five years ago, in an email I sent to a group of experts before a Workshop at the 13th Conversation at Albany (NY):
   

   Looking back, 3DNA has never been intended to set up a new standard for the exact definition of various parameters. We selected what made best sense to us from what were already available. This was made possible by knowing the exact technical details of how other programs work. In the meantime, 3DNA also provide a program called "cehs" which gives the original CEHS/SCHNAaP parameters, to which Freehelix parameters would be similar. Believe it or not, "cehs -r" would give the authentic RNA parameters. We also see Curves unique in defining global parameters, bending analysis and groove dimensions."

2. Active support through emails and the 3DNA forum. Over the years, I have always striven to get back to each 3DNA-related question quickly and concretely. In my memory, I have never ignored users' questions. Instead, I have taken each and every question as a way to improve 3DNA, and refined the code accordingly.
3. 3DNA's integrated approach that incorporates structural analysis, modeling building, and visualization in a single suite of software package. Our 2008 Nature Protocols paper provides some examples.
4. 3DNA has been extensively checked against all NDB entries before each major release, so that I can confidently say that it works in real world, not just in some contrived limited example cases.

I still remember that the number of citations to 3DNA was less than 150 nearly two years ago, when I started to wrote the first draft of our 2008 Nature Protocols paper. Now it is more than doubled! I would blog on this topic again when the number reaches 500.

In my opinion, some of 3DNA features are still (heavily) underused. Now that we have a sizable user community, 3DNA could only become better and would be more widely used. I have every reason to believe that in the not-so-distant-future, the citations to 3DNA would reach over 1000.

For current status of 3DNA citations, check Google Scholar.