1. DNA / RNA Double helix modelling using dinucleotides as building blocks

• Upload FASTA format input sequence
   

Sample DNA Sequence file, Sample RNA Sequence file


• Is 3-ATOM fast generation option required?
Yes No


• Enter fragment length for calc the bending angle: [Default is 10]

• Parameters selection based on molecule type
  

For DNA Helix
Use standard BDNA fiber model dinucleotide parameter file
Use standard ADNA fiber model dinucleotide parameter file
Use standard DNA CRYSTAL.LOC dinucleotide parameter file
Use standard DNA BOLSHOY.LOC dinucleotide parameter file
User defined DNA parameter file
For RNA Helix
Use standard ARNA fiber model dinucleotide parameter file
Use standard A'RNA fiber model dinucleotide parameter file
Use free RNA crystal data derived dinucleotide parameter file
User defined RNA parameter file

Sample DNA parameter file, Sample RNA parameter file


     

2. Regeneration

Select molecule Type

DNA RNA



Please upload a LOC file in the prefered format:


Sample DNA regen file ,  Sample RNA regen file

     

In case you want to regenerate a DNA or RNA PDB structure use NUPARM program to generate the PRM output file and create a LOC file with defined format as above.
The backbone discontinuity can be corrected by minimizing the backbone, while holding rest of the basepair using restraints. For regeneration, the Run_minimization.pl script is activated and produces the *_minimized.pdb structure. See  About for more  details.

 NUPARM Program web-server link