NUPARM-Plus
A Program for analysis of the geometry of nucleic acid duplexes

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.

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Pre-compiled results for the representative examples, mentioned in the first table of Dataset Used section (Only default options are used ):
Select any PDB ID 1BNA 1R2L 1CDW 1ZEX 4OCB 1QC0

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For single PDB file: [?]
Please enter PDB-ID code of the DNA/RNA molecule:
Alternatively, you can upload a PDB format file:
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Base pairing information: [?]
Upload the INPUT file containing base pairing information or choose BPFIND: [Default is the BPFIND]
Select the base pairing record to be used BPFIND USER DEFINED (file upload) USER DEFINED (start and end nucleotide numbers) BPFIND will be used for identifying the base-pairs. BPFIND Will be used for identifying base-pairs. DSSP assigned alpha helices alongwith Pi & 310 helices (length greater than 6) will be considered for HELANAL-Plus run. 5' to 3' nucleotide number along with the corresponding chain ID for both the strands of a duplex should be given in the format 21:A (21 is nucleotide number and A is chain ID). Only Watson-Crick base pairing will be assigned to the base-pairs. Strand 1      -    Strand 2      -    Strands are parallel    anti-parallel Helix Information available in the input PDB file will be considered for the HELANAL-Plus run.         Example File Base pairing information of more than one duplex can also be provided. Each duplex must be terminated by a line consisting of " 0" (four spaces). The uploaded 3D coordinate file must contain only the constituent atomic coordinates of nucleic acids. Nucleotide numbers given in the uploaded duplex information file will be considered as the serial number of the nucleotides in the uploaded coordinate file. Details can be found in the help page .
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Available Options: [?]
Define the Y-axis line as:	C6-C8  C1' - C1'
Reorient the molecule about a 'Linear Global Axis' fitted to:
Local HELIX ORIGINS Base-Pair CENTERS Other Backbone atom (Choose the atom type) C1' C2' C3' C4' C5' P 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
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