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.
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.
- 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)
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