A Program for analyzing sequence dependent variations in nucleic acid (DNA & RNA) double helices

NUPARM-Plus is a program to analyze and characterize overall geometry of input double stranded helices. This program can be very useful in understanding sequence directed structural variations in nucleic acids. It can also be used in the modeling of nucleic acid helices, analysis of molecular dynamics runs of structures containing double stranded helices etc. This web server version of NUPARM-Plus uses JmolApplet to display the double stranded helices along with their axis, in the same orientation as that in the input pdb file. Jmol is a Java applet and hence the web browser must have the Java plugin properly installed and enabled.

For single PDB file:
   Please enter PDB-ID code of the DNA/RNA molecule:
   Alternatively, you can upload a PDB format file:

Base pairing information:
Upload the INPUT file containing base pairing information or choose BPFIND:
[Default is the BPFIND]

Available Options:
   Define the Y-axis line as: C6-C8  C1' - C1'

   Reorient the molecule about a 'Linear Global Axis' fitted to:
  • Base-Pair CENTERS
  • Other Backbone atom (Choose the atom type)
  • Not Required
   Are P--P distances and Cylindrical Polar Coordinates required?
Yes No
(Only meaningful if the molecule is reoriented ; P--P distance is needed to calculate groove width)
   Is the Backbone and Sugar torsion angle parameters required?
Yes No
   Is the calculation of stacking overlap required? (Will significantly slower the program)
Yes No
   Are Single Strand parameters required?
Yes No
   Select Option for helix axis display
Local helix origin points
Points on the best fit 3D line / Sphere fitted to the local origin points

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