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 (available via pip install)

RNA 3D Structure Alignment

ARTEM - a tool for RNA tertiary motif search. DOI: 10.1186/s13059-025-03696-2

ARTEMIS - a tool for RNA 3D Structure Alignment. DOI: 10.1093/nar/gkae758 (Demo, Tutorial)

Other Tools and Datasets

ContExt - a lightweight and fast utility for obtaining atom-atom contacts from PDB/mmCIF files DOI: 10.1101/2025.05.30.657037 (Demo)

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

GNRA - A dataset of GNRA tetraloop-like RNA 3D modules. DOI: 10.1038/s41598-025-21072-9

ARTEM-KT - A dataset of kink-turn-like RNA 3D modules. DOI: 10.1186/s13059-025-03696-2

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

JAR3D - scoring RNA loop sequences against known 3D motifs. DOI: 10.1093/nar/gkw453

ModeRNA - a tool for comparative modeling of RNA 3D structure. DOI: 10.1093/bioinformatics/btr400

SimRNA - a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories. DOI: 10.1093/nar/gkae356

QRNAS - software tool for refinement of nucleic acid structures. DOI: 10.1186/s12900-019-0103-1

RNAComposer - an automated template-based RNA structure modeling server. DOI: 10.1007/978-1-4939-6433-8_13

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