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RNAHelix Server



Write or paste RNA sequence with pair type:[help]GCWWC
AAwwC
GCWWC
AGHST
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Server Overview

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 et al. (2017) J. Comp. Aided. Mol Des. 31: 219-235". The values of these parameters are obtained from the associated RNABPDB databases as mean parameters of the chosen basepairs and the dinucleotide steps.

Please type the sequence of the desired RNA double helical structure along with basepairing patterns of each basepair without any punctuation mark. 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:

GCWWC

AAHST

UGWWC

AUWWC

If you make use of the data presented here, please cite the following articles in addition to the primary data sources:



Contact for Corrospondance
RNABPDB & RNAHelix © Comp Sci Div, SINP Kolkata 2017
Protein Data Bank NDB Nucleic Acid Database RNA Base Pair Count Geometry and Stability RNA Base Pair Database Nucleic Acid Nomenclature and Structure