Calculate the global 3D structure of a DNA molecule from its nucleotide sequence according to the dinucleotide wedge model. Analyze local bending angles and macroscopic curvature.

Try the Kinetoplast or Phased AAAAAA sequences for example.

For each nucleotide at position *i* of the sequence,
the following values are calculated:

- the
**3D coordinates**of the helix axis and 5' Phosphate atoms of a B-DNA. - the
**curvature**, which is the inverse of the radius of a circle passing through helix axis coordinates at*i*-10,*i*, and*i*+10. - the
**curvature angle**between the smoothed basepair normal vectors at*i*-15 and*i*+15. - the local
**bend angle**between the basepair normal vectors at*i*-2 and*i*+2.

The curvature and bend angles are normalized to the curvature in a nucleosome.

**Output files** of the analysis are:

- a plot of the helix backbone coordinates and curvature values.
- all calculated values in CSV format.
- the helix backbone coordinates in PDB format.

### References

- Curved DNA
without A-A: experimental estimation of all 16 DNA wedge angles.

Bolshoy A. et al; Proc Natl Acad Sci USA 88; 2312-6 (1991) - Bending and
curvature calculations in B-DNA.

Goodsell DS; Dickerson RE; Nucleic Acids Res 22; 5497-503 (1994) - A comparison
of six DNA bending models.

Tan RK; Harvey SC; J Biomol Struct Dyn 5; 497-512 (1987) - Curved DNA:
design, synthesis, and circularization.

Ulanovsky L. et al; Proc Natl Acad Sci USA 83; 862-6 (1986)

### Disclaimer

Because this service is provided free of charge, there is no warranty for the service, to the extent permitted by applicable law. The service is provided "as is" without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance is with you.

### Credits

Developed by Christoph Gohlke, Laboratory for Fluorescence Dynamics. Source code is available under BSD license: dnacurve.py and dnacurve_cgi.py