RNAHelix Server

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.

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:

GCWWC

AAHST

UGWWC

AUWWC

The server would generate the input file, from RNABPDB as mean values of the selected base pairs or base pair steps, for running RNAHelix program and would allow the users to confirm or adjust the parameters. This is important as structural parameters of few base pairs and some base pair steps are not sufficient in the database. These insufficient data may need to be confirmed by the user's additional data. Furthermore, often bimodal distributions of some parameters, especially Shear for some base pairs was noted, where the mean value cannot be used for structure generation. The users are recommended to view the database and decide the parameters suitable for his/her perpose and model accordingly. These cases are highlighted in different color in the input file.
Once the user clicks Save & Proceed button the program generates structures of base pairs of the choosen double helix. Finally CHARMM is used to run constrained energy minimization to obtain suitable coordinates of sugar-phosphate backbone.

1. RNABPDB: Molecular Modeling of RNA Structure—From Base Pair Analysis in Crystals to Structure Prediction.
   Mukherjee, D., Maiti, S., Gouda, P.K. et al. Interdiscip Sci Comput Life Sci 14, 759–774 (2022).
2. RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.
   Bhattacharyya D, Halder S, Basu S, Mukherjee D, Kumar P, Bansal M. J Comput Aided Mol Des. 2017 Feb;31(2):219-235.
3. Analysis of stacking overlap in nucleic acid structures: algorithm and application.
   Pingali, P.K., Halder, S., Mukherjee, D. et al. J Comput Aided Mol Des 28, 851–867 (2014)
4. Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis.
   Mukherjee S, Bansal M, Bhattacharyya D. J Comput Aided Mol Des. 2006 Oct-Nov;20(10-11):629-45.
5. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures.
   Bansal M, Bhattacharyya D, Ravi B. Comput Appl Biosci. 1995 Jun;11(3):281-7.
6. A Self-Consistent Formulation for Analysis and Generation of Nun-Uniform DNA Structures.
   Bhattacharyya and M. Bansal (1989) J. Biomol. Struct. Dynam. 6, 645-653.
7. Definitions and nomenclature of nucleic acid structure components,
   R.E. Dickerson, Nucleic Acids Res. 17 (1989) 1797–1803.

RNAHelix is a software that regenerates RNA three dimensional structures from base-pair information.

Software Download (Linux Distribution):
The linux distribution of the RNAHelix software can be downloaded from this link.

This Distribution Includes:

1. RNAHelix.linux: The executable binary for linux.
2. RNAHelix.f: The source code.
3. README: The Installation guide as well as user manual.
4. LICENSE: The GNU GPL License file.
5. sample: A directory that contains sample output.
6. DataSet.dat
7. prm2param.pl
8. parameter.loc
9. par_all27_na.inp
10. top_all27_rna.inp
11. top_all27_dna.inp
12. minimize.inp

Note: The files from 6-12 are required to run the system properly. Follow the README file for their usage.