1. DNA / RNA  duplex modelling building: NUCGEN-Plus program builds DNA  and RNA duplexes for a given input sequence.

  • The input sequence is given in a FASTA format. Sample sequence files ( DNA , RNA )
  • Model building options : The model can built using dinucleotide step and intra-basepair parameters obtained from crystal structures.
For DNA molecule:
a. Crystal.loc ( Nagaich et al 1994 )
b. Bolshoy.loc ( Bolshoy et al 1991)

For RNA molecule:
a. A-RNA fibre model (Arnott, pp1-38; Oxford Handbook of Nuc. Acids 1999)
b. A'-RNA fibre model ( -do-)
c. crystal_RNA.loc (Senthilkumar et al 2013)

  • An option is available to generate a C1' atom alone containing duplex structure, useful for very long sequences (3 Atom fast generation).
  • One can specific the fragment length to be used for bending angle calculation if required.
  • Users can also input their own parameter file in the given template format. Sample parameter LOC files ( DNA , RNA )

2. Double helix regeneration: NUCGEN-Plus program can regenerate duplexes from dinucleotide and basepair parameter of a given double helical DNA or RNA.  This features help in generating geometrically altered duplex structures.
  • The basepair and step parameters information along with basepair details of any helix can be given as input.
  • See sample input files. Sample regeneration parameter LOC files ( DNA , RNA   )
  • Intial parameter information has to be derived by analysing the duplex using NUPARM program.
  • Prm2Loc.pl script can extract necessary information from PRM file and generate the necessary LOC file.
File content:

1.  FASTA contains the input sequence information (only for building option)
2.  LOC contains the input parameter information (only for regeneration opion)
3.  COR contains the output coordinate.
4.  CIF contains CIF formated coodrinates.
5.  HLX contains C1' atoms alone (only for 3-atom fast regeneration option)
6.  BPC contains basepair centers.
7.  ANG contains bending angle values.
8.  warning.txt This file contains a warning message on using COR files, in case of long duplexes. COR file has coordinates written in PDB format, which has limitation on coordinate character length. So our program generates CIF file which is free of this limitation. Common visualization tools like PyMol can be used to visualize CIF formatted files.

For example:

user@localuser# cat warning.txt
*** ATOM coordinate length limit exceeded in COR file***
Use CIF file instead

Minimization of phosphate backbone:: The backbone conformation of the nucleotide coordinates is fixed in standard B-form conformation. This at times can cause break in the backbone connectivity. This can be corrected by minimizing the phopshate backbone while the rest of the base and sugar atoms are restrained. A sample code using NAB (Nucleic Acid Builder) to minimize is provided herein. Run_minimization.pl . The code assumes that OPENBABEL and AMBERTOOLS13 is installed and the path is correctly mentioned in the script. Please cite NAB and AMBERTOOLS13, if using this script for minimizing the backbone.