Four papers in the August 2012 [40(14)] issue of NAR cite 3DNA

While browsing the August 2012 40(14) issue of Nucleic Acids Research (NAR), I noticed the following four papers that cite 3DNA:

The local base pair step parameters as calculated by x3dna (37,38) are represented in the Supplementary Figure S2.

The initial extended single-stranded DNA structure was obtained using the 3DNA program (15).

DNA structures were analyzed using 3DNA (31).

Each of these DNA structural models consists of values for all base-pair step parameters (roll, twist, tilt, rise, shift and slide) for each dinucleotide or trinucleotide. This enabled us to convert DNA sequences into 3D coordinates by using the rebuilding part of 3DNA (39), a program for analysis, rebuilding and visualization of 3D nucleic acid structures.

The above four NAR papers appear in the sections “Nucleic Acid Enzymes” (1), “Structural Biology” (2) and “Methods Online” (1), and cover research areas of DNA-protein interactions (3) and G-quadruplex structures (1). As quoted above, two papers employ the analyzing components of 3DNA, while the other two take advantage of its rebuilding facilities.

Between the two primary 3DNA publications, the 2003 NAR paper (NAR03) is cited twice, while the 2008 Nature Protocol paper (NP08) is cited three times. Apparently, after some time lag, NP08 has gradually overpassed NAR03 to become the community’s favorite citation for 3DNA.





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