Our works

RNA Secondary Structure Prediction

SQUARNA - an RNA secondary structure prediction method based on a greedy stem formation model. DOI: 10.1101/2023.08.28.555103

RNA 3D Structure Alignment

ARTEM - a tool for RNA tertiary motif search. DOI: 10.1093/nar/gkad605

ARTEMIS - a tool for RNA 3D Structure Alignment. DOI: 10.1093/nar/gkae758

Other Tools and Datasets

urslib2 - a Python library for processing RNA structure data from PDB/mmCIF files & DSSR annotations. DOI: 10.1093/nar/gkad605

LORA - A dataset of long-range RNA 3D modules. DOI: 10.1093/nar/gkad605

ARTEM-KT - A dataset of kink-turn-like RNA 3D modules. DOI: 10.1101/2024.05.31.596898

RNA-related hints

• Expect ~80% of all Mg ions in RNA-containing 3D structures to be garbage

• Rfam families of riboswitches are usually aptamer-only and don't include the platforms

Not our works, but still worth it :)

RNA CoSSMos - a database of RNA 3D loop motifs. DOI: 10.1093/database/baz153

Rclick - a tool for topology-independent RNA 3D structure alignment. DOI: 10.1093/nar/gkw819

US-align - a unified protocol to compare 3D structures of different macromolecules. DOI: 10.1038/s41592-022-01585-1

RNA3DHub - RNA Structure Atlas, RNA 3D Motif Atlas, and Representative RNA Sets. DOI: 10.1016/j.ymeth.2016.04.025

DSSR - Dissecting the spatial structure of RNA, annotation of RNA interactions. DOI: 10.1093/nar/gkv716

RNA-related Wikipedia pages

https://en.wikipedia.org/wiki/Category:RNA

https://en.wikipedia.org/wiki/RNA

https://en.wikipedia.org/wiki/Nucleic_acid_structure

https://en.wikipedia.org/wiki/Nucleic_acid_tertiary_structure

https://en.wikipedia.org/wiki/Structural_alignment_software

https://en.wikipedia.org/wiki/Nucleic_acid_structure_prediction

https://en.wikipedia.org/wiki/Nucleic_acid_secondary_structure

https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

https://en.wikipedia.org/wiki/Nucleic_acid_thermodynamics

https://en.wikipedia.org/wiki/Internal_loop

https://en.wikipedia.org/wiki/Stem-loop

https://en.wikipedia.org/wiki/Pseudoknot

https://en.wikipedia.org/wiki/Tetraloop

https://en.wikipedia.org/wiki/Nucleic_acid_double_helix

https://en.wikipedia.org/wiki/RNA_motif