A Program for analysis of the geometry of nucleic acid duplexes

Please let the cursor hover over the option headers ([?]) for hints.

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 dynamic trajectories of structures containing double stranded helices etc. This web server version of NUPARM-Plus uses JSMol (JmolApplet) to display the double stranded helices along with their axis, in the same orientation as that in the input pdb file.

Pre-compiled results for the representative examples, mentioned in the first table of Dataset Used section (Only default options are used ):

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 Cylindrical Polar Coordinates required?
Yes No
(Only meaningful if the duplex is reoriented)
   Is the Backbone and Sugar torsion angle parameters required?
Yes No
   Is the calculation of stacking overlap required? (Will significantly slow the program)
Yes No
   Are Single Strand parameters required?
Yes No
   Select Option for duplex global axis display
Local origin points
Points on the best fit 3D line / Sphere fitted to the local origin points

Questions or problems regarding this web site should be directed to [].
Copyright © 2010 [Molecular Biophysics Unit,IISC]. All rights reserved.