RNAsolo 2.0: multimodal database to study RNAs, their structural families and intermolecular interfaces.

Understanding RNA structures - essential for uncovering their biological functions, interactions, and therapeutic potential - relies on both experimental techniques and computational approaches increasingly driven by artificial intelligence. The latter are transforming RNA structural research but depend on large, reliable datasets, which remain limited, particularly for RNA-protein and RNA-DNA complexes. To address this gap, we present RNAsolo 2.0 ( https://rnasolo.cs.put.poznan.pl/), an open-access database integrating cleaned, non-redundant RNA 3D structures with detailed information on their intermolecular interactions. Building on the original RNAsolo, which has attracted over 16,000 page views from ∼5,600 users, this release adds Rfam-based family classification, >2,500 precompiled benchmark sets, and multimodal representations encompassing sequence, secondary and tertiary structure, as well as torsion angle data. RNAsolo 2.0 enables searches for RNAs that interact with specific proteins, ligands, or ions, and provides an interactive view of their binding interfaces. The tool offers a robust, user-friendly platform for RNA structural biology and next-generation AI-driven modeling.

• Publication year

  2025

• Venue

  Journal of Molecular Biology

• Publication date

  2025-11-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1016/j.jmb.2025.169570PMID 41320116
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Has AlphaFold3 achieved success for RNA?

  2025cited by this paper
• DSSP 4: FAIR annotation of protein secondary structure

  2025cited by this paper
• Graph neural network and diffusion model for modeling RNA interatomic interactions

  2025cited by this paper
• The RNA‐Puzzles Assessments of RNA‐Only Targets in CASP16

  2025cited by this paper
• RNAtango: Analysing and comparing RNA 3D structures via torsional angles

  2024cited by this paper
• Rfam 15: RNA families database in 2025

  2024cited by this paper
• Knotted artifacts in predicted 3D RNA structures

  2024cited by this paper
• RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction

  2024cited by this paper
• State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction

  2024cited by this paper
• Assessment of three‐dimensional RNA structure prediction in CASP15

  2023cited by this paper
• When will RNA get its AlphaFold moment?

  2023cited by this paper
• RNA target highlights in CASP15: Evaluation of predicted models by structure providers

  2023cited by this paper
• RNAsolo: a repository of cleaned PDB-derived RNA 3D structures

  2022cited by this paper
• fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions

  2021cited by this paper
• Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

  2021cited by this paper
• Entanglements of structure elements revealed in RNA 3D models

  2021cited by this paper
• Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

  2021cited by this paper
• RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures

  2020cited by this paper
• RNApolis: Computational Platform for RNA Structure Analysis

  2019cited by this paper
• Blind prediction of noncanonical RNA structure at atomic accuracy

  2017cited by this paper
• A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

  2016cited by this paper
• MCQ4Structures to compute similarity of molecule structures

  2013cited by this paper
• Structural basis of initial RNA polymerase II transcription

  2011cited by this paper
• Biopython: freely available Python tools for computational molecular biology and bioinformatics

  2009cited by this paper
• FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

  2007cited by this paper
• The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

  2006cited by this paper
• Geometric nomenclature and classification of RNA base pairs.

  2001cited by this paper

• No citing papers are available for this paper.