SimRNA prediction (left) vs native structure (right) of Viral RNA Psedoknot.

PDB id: 1l2x, RMSD = 2.79Å

SimRNA uses reduced representation of residues.

Residues are represented five pseudoatoms - green represents the backbone and red represents the base moieties.

The full atom structure (left) vs the SimRNA reduced representation (right).

SimRNA prediction of 1l2x.

The energy landscape generated in the course of a set of SimRNA simulations.

Results are shown for the gene 32 messenger RNA pseudoknot of bacteriophage T2 (PDB id: 2tpk)

SimRNA is a method for RNA 3D structure modeling with optional restraints.
SimRNA uses (1) a coarse-grained representation, (2) relies on the Monte Carlo method for sampling the conformational space, and (3) employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures.

What's new?

1. Incorporation of diverse restraints: Users can now implement a broader range of restraints, encompassing both canonical and non-canonical base pairs, and unpaired residues, as well as data from chemical probing experiments.
   • Soft restraints on secondary structure [Dec. 2023]
   • Hard restraints on base pairs [Dec. 2023]
   • Soft restraints on base pairs [Dec. 2023]
   • restraints on Chemical probing data [Dec. 2023]
   • exclude Watson-Crick edge for base pairing [Dec. 2023]
2. Advanced control over simulation parameters: A new way of defining restraints that can help model alternative RNA structures and increased control over simulation parameters, enabling the simulations of conformational space searching, folding, and unfolding. [Dec. 2023]
3. Enhanced data processing and analysis: Improved data processing capabilities, with a wider array of options for clustering folding trajectories and generating representative models, and reanalyzing the same simulation multiple times using different parameters, facilitating a more thorough exploration of RNA folding landscapes [Dec. 2023].

For more see the Tutorial

To download a standalone version of SimRNA, visit https://genesilico.pl/software/stand-alone/simrna/

References

SimRNAweb v2.0: A web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories  
S. Naeim Moafinejad, Belisa R H de Aquino, Michał J. Boniecki, Iswarya P N Pandaranadar Jeyeram, Grigory Nikolaev, Marcin Magnus2, Masoud Amiri Farsani, Nagendar Goud Badepally, Tomasz K. Wirecki, Filip Stefaniak, Janusz M. Bujnicki
Nucleic Acids Res 2024 [doi: 10.1093/nar/gkw279]

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints
Magnus M*, Boniecki MJ*, Dawson W, Bujnicki JM
Nucleic Acids Res 2016 [doi: 10.1093/nar/gkae356]

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM
Nucleic Acids Res 2015 [doi: 10.1093/nar/gkv1479]