overlapping area calculation - stacking interactions

[Agnieszka]

Hi,

I used new online xdna-dssr server and got calculated parmeters. However I can't see anymore the calculation of overlapping area as used to be in older version which I liked it very much. Is this option still available?

Agnieszka

[xiangjun]

Hi Agnieszka,

Thank you for using 3DNA/DSSR and for sharing your feedback.

The new wDSSR website introduces several modernized features, though a few specialized analyses from the legacy 3DNA 2.0 web server were initially omitted to keep the interface streamlined. Based on recent user requests, we have already restored backbone torsion angles to the wDSSR platform.

Regarding the base-pair overlapping area: this metric is calculated by the underlying DSSR engine but is not yet rendered on the wDSSR web server. In the meantime, you can obtain these overlapping areas directly by running the DSSR command-line program locally.

We are happy to integrate this feature into the web platform. Which format would best fit your workflow? For instance, would adding a dedicated section to the downloadable wDSSR output file be sufficient?

Code: [Select]

Overlap area in Angstrom^2 between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the designed base-pair step.

Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and
inter-strand overlap is designated according to the following diagram:

                    i2  3'      5' j2
                       /|\      |
                        |       |
               Strand I |       | II
                        |       |
                        |       |
                        |      \|/
                    i1  5'      3' j1

     step      i1-i2        i1-j2        j1-i2        j1-j2        sum
   1 CG/CG  1.48( 0.00)  0.00( 0.00)  0.97( 0.00)  0.94( 0.00)  3.39( 0.00)
   2 GC/GC  2.95( 0.63)  0.00( 0.00)  0.00( 0.00)  0.96( 0.04)  3.91( 0.68)
   3 CG/CG  2.66( 0.00)  0.00( 0.00)  0.15( 0.00)  3.44( 0.21)  6.25( 0.21)
   4 GA/TC  3.94( 1.11)  0.00( 0.00)  0.00( 0.00)  4.17( 0.78)  8.11( 1.88)
   5 AA/TT  3.51( 2.16)  0.00( 0.00)  0.00( 0.00)  5.09( 0.08)  8.60( 2.24)
   6 AT/AT  5.91( 2.14)  0.00( 0.00)  0.00( 0.00)  5.65( 1.89) 11.56( 4.03)
   7 TT/AA  5.08( 0.11)  0.00( 0.00)  0.00( 0.00)  3.68( 2.39)  8.76( 2.51)
   8 TC/GA  2.20( 0.00)  0.00( 0.00)  0.00( 0.00)  4.98( 2.19)  7.18( 2.19)
   9 CG/CG  5.50( 1.17)  0.00( 0.00)  0.01( 0.00)  1.56( 0.00)  7.06( 1.17)
  10 GC/GC  0.57( 0.00)  0.00( 0.00)  0.00( 0.00)  5.32( 2.35)  5.89( 2.35)
  11 CG/CG  0.73( 0.00)  0.00( 0.00)  0.54( 0.00)  1.98( 0.03)  3.25( 0.03)
Best regards,

Xiang-Jun

[Agnieszka]

Yes, please. That would be convenient to have it as downloadable wDSSR file.
Thank you,
Agnieszka