This server uses Intra-basepair (Buckle, Open, Propeller, Stagger, Shear and
Stretch) and Inter-basepair parameters (Tilt, Roll, Twist, Shift, Slide and
Rise) for given basepairs and basepair dinucleotide steps, respectively, for
model building structure of an RNA double helix. The procedure was explained with few examples by
showing accuracy of the models in "Bhattacharyya
The RNAHelix software uses all Intra Base Pair parameters (Buckle, Open, Propeller, Stagger, Shear and Stretch)
of each base pair (canonical Watson-Crick type
or non-canonical type) and all the Inter Base Pair parameters (Tilt, Roll, Twist, Shift, Slide and Rise)
of each dinucleotide step. Hence, it uses
N x 6 Intra base pair parameters and (N-1) x 6 Inter base pair parameters. These values are obtained
from the associated RNABPDB database as mean values of all the chosen base pairs and steps.
The sequence of the RNA along with base pairing scheme is required for structure generation as for most RNA double helical structures base complementarity is not maintained. Hence sequence of both the strands are important along with base pairing edges forming hydrogen bonds. The first line should contain the first basepair (left one at the 5'-end of first strand and right one appearing at the 3'-end of the second strand) and so on. Please note the basepairing patterns are case sensitive, i.e. HST is different from hsT. Hence for generation double helix with G:C W:WC, A:A H:ST, U:G W:WC and A:U W:WC basepairs with first strand having 5'-(GAUA) and second strand having 5'-(UGAC) sequences please write the sequence as:
RNAHelix is a software that regenerates RNA three dimensional structures from
Software Download (Linux Distribution):
The linux distribution of the RNAHelix software can be downloaded from this link.
This Distribution Includes: