ABOUT THE PROGRAM:

a) Standalone version
b) Web-version

 The NUPARM program has been developed so as to meet most of the requirements stipulated at the EMBO Workshop on DNA Curvature and Bending, held at Cambridge, U.K., in Sept. 1988. The Nomenclature and Description of the DNA structural parameters follows the Cambridge Convention ( Dickerson 1989,NAR )


1.  Base step and base pair parameters:

  • Local step parameters (w.r.t. a helix axis for each doublet step)
Tilt, Roll, Twist, Shift, Slide and Rise.
  • Local helical parameters (w.r.t. a helix axis for each doublet step)
Inclination, Tip, Helical Twist, Displacements (dx and dy) and Helical Rise (dz).
  • Intra-base pair parameters:
Virtual glycosidic bond angles: between the two glycosidic bonds (N--C1') and the C1'--C1' vector are also given. The Intra-basepair C8--C6 and C1'--C1' distances are also listed
* Opening angle is defined as the angle between the lines C1'--C8 and C1'--C6 projected on to the mean base-pair plane.
  • Global helical parameters: (w.r.t. a single global helix axis for the whole Helix)
Inclination, Tip, Helical Twist, Displacements (dx and dy) and Helical Rise (dz).

2.  Single-strand parameters: (for strand 1 and strand 2)
  • Local Step Parameters:
  • Single Strand Parameters with New Definition of Base fixed axes:
      1. Local Step Parameters:
      2. Local Helical Parameters:
      3. Global Helical Parameters:
3.  Phosphate polar coordinates & C1' cylindrical polar coordinates
The cylindrical polar coordinates of the phosphate and C1' atoms are calculated by assuming the global axis to be the Z-axis,
4.  Inter-chain P--P anc C1'-C1'  distances
The intra and inter-chain phosphate distances are also listed, for P and C1' atoms. 
5.  Backbone and Glycosidic Torsion Angles
The torsion angles is used, then the main chain torsion angles, the glycosidic torsion angles and the furanose ring, endocyclic torsion angles are printed. The sugar pucker phase angle and amplitude of puckering (as described in Harvey and Prabhakaran, J. Amer. Chem. Soc. 1986) are listed along with the ring torsion angles. This calculation is the most time consuming part of the analysis program.

6. Additional information:
The direction cosines of the local helix axes and base-pair normals as well as  the coordinates of local helix origins and base-pair centers are printed. The angle between each local helix axis and all others, as also the angles between base-pair normals are tabulated. Algorithm:

Only the purine/pyrimidine ring atoms are included when calculating the base normals. We found only a nominal difference in the parameters when all the pendant atoms are included. The mean base-pair normal is taken to be the average of the two normals in the base-pair, in order to minimize the differences due to the size of the purine and pyrimidine rings.

The 5'-->3' direction of strand 1 is used to define the positive Z-direction and the Y-axis is taken as pointing towards this strand. The X-axis then points towards the major groove, as suggested in the Cambridge Convention( Dickerson 1989, NAR). The base-pair center is defined as the midpoint of C6 and C8 atoms of pyrimidines and purines respectively. The long axis (Y-axis) can be along the C6---C8 direction and passes through the base-pair center.

The definition of the local helix and wedge parameters are in terms of the local helix axis and the mean Z-axis respectively for the doublet involved (as described by Bhattacharyya et al J. Biomol. Struct. Dynam.,1989 ). In this description the signs of tilt, tip and buckle were opposite to the Cambridge definition. Subsequently the algorithm has been modified so as to follow the Cambridge Convention, wherein all clockwise rotations are positive when viewed down the rotation axis.

INPUT TO THE PROGRAM:
    The input file name for the nucleic acid double helix structure to be analyzed has to be specified first. If an existing PDB filename is given, the file will be picked up from the local PDB server at IISc. Alternatively the user can browse on their own computer and click on the filename to be used.

The program next asks whether the nucleotides in the duplex are numbered according to the standard PDB 5'-->3' residue numbering scheme, with the first nucleotide base paired to the last base. If not, the file containing a user-defined, residue numbering scheme has to be specified (eg. if an AMBER output is being used, or the file has base overhangs, bulges etc, such that it is only partially paired as in tRNA and many other structures). This option can also be used to analyze duplexes in protein-DNA complex structures, if the residue numbers are unique. The residue numbers of paired bases have to be given in (I5, 1x, I5) format for a duplex.

The helix can be reoriented to give the base-pair parameters with respect to a global axis. The realignment is done in two steps: (i) the best line is fitted (by the method of least squares) to a set of representative points taken either from all the residues, or the doublet steps. The molecule is rotated such that this line becomes parallel to the global Z-axis. (ii) The same representative points are used to find the mean point through which the line passes, and the molecule is translated such that this point coincides with the origin and the best line with the Z-axis.
There are several options available for choosing the representative points. The user may choose between

  • the local helix origins for each of the doublet steps
  • the base-pair centers or
  • any atom in the backbone.
The user can also leave the molecule in the original orientation, but then NUPARM may not give proper values for global helical parameters as well as cylindrical polar coordinates for P and C1' subsequently.

The options to calculate P--P and C1'--C1' cylindrical polar coordinates, the intra and inter chain distances for these atoms, all backbone and sugar ring torsion angles, as well as inter base parameters in each strand are also available.

OUTPUT FILES
 NUPARM generates two output files

  1. PRM files: contains all the calculated parameters as mentioned above.

  2. COOR file Its is created only when the option of reorienting the molecule about the global helix axis is used. It contains the transformed coordinates, as well as related residue and atom information. It can also be used as input for NUPARM.
 

Note:
  1. In the web version of NUPARM the various options available in the original version of NUPARM have been restricted to standard ones.
  2. Coordinates of multiple helices (minimum 4 basepairs) are automatically extracted and provided in individual files for structures with more than one helices. e.g. tRNA.