- ‘Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease’ by Elena Manakova et al.:
The local base pair step parameters as calculated by x3dna (37,38) are represented in the Supplementary Figure S2.
- ‘Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops’ by Maja Marusic et al.:
The initial extended single-stranded DNA structure was obtained using the 3DNA program (15).
- ‘Non-specific protein–DNA interactions control I-CreI target binding and cleavage’ by Rafael Molina et al.:
DNA structures were analyzed using 3DNA (31).
- ‘A flexible integrative approach based on random forest improves prediction of transcription factor binding sites’ by Bart Hooghe et al.:
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.