ArticleRNA (New York, N.Y.)2022
RNALigands: a database and web server for RNA-ligand interactions.
Article in RNA (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 38 citations in OpenAlex.
- In silico designing of small molecules for targeting RNA: current landscape and future directions.Journal of computer-aided molecular design · 2026Review
- Machine Learning for RNA-Targeting Drug Design.Journal of chemical information and modeling · 2026Review
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- NMR-Based Fragment Screening for RNA-Targeted Drug Discovery.Molecules (Basel, Switzerland) · 2026Review
- DeepRNA-DTI: a deep learning approach for RNA-compound interaction prediction with binding site interpretability.Journal of cheminformatics · 2025Article
- DistRMI: a deep distance-aware neural network for explainable RNA loop motif-small molecule interaction prediction.Briefings in bioinformatics · 2025Article
- Review
- In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2.Scientific reports · 2025Article
- RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation.Nucleic acids research · 2025Article
- Advances and Mechanisms of RNA-Ligand Interaction Predictions.Life (Basel, Switzerland) · 2025Review
- Harnessing Computational Approaches for RNA-Targeted Drug Discovery.RNA nanomed · 2024Article
- SMTRI: A deep learning-based web service for predicting small molecules that target miRNA-mRNA interactions.Molecular therapy. Nucleic acids · 2024Article
- Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN.Nature communications · 2024Article
- Advances in machine-learning approaches to RNA-targeted drug design.Artificial intelligence chemistry · 2024Article
- Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction.Bioinformatics (Oxford, England) · 2024Article
- Targeting MicroRNAs with Small Molecules.Non-coding RNA · 2024Review
- Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.RNA (New York, N.Y.) · 2023Article
- Review
- R-BIND 2.0: An Updated Database of Bioactive RNA-Targeting Small Molecules and Associated RNA Secondary Structures.ACS chemical biology · 2022Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA molecules can fold into complex and stable 3D structures, allowing them to carry out important genetic, structural, and regulatory roles inside the cell. These complex structures often contain 3D pockets made up of secondary structural motifs that can be potentially targeted by small molecule ligands. Indeed, many RNA structures in PDB contain bound small molecules, and high-throughput experimental studies have generated a large number of interacting RNA and ligand pairs. There is considerable interest in developing small molecule lead compounds targeting viral RNAs or those RNAs implicated in neurological diseases or cancer. We hypothesize that RNAs that have similar secondary structural motifs may bind to similar small molecule ligands. Toward this goal, we established a database collecting RNA secondary structural motifs and bound small molecule ligands. We further developed a computational pipeline, which takes as input an RNA sequence, predicts its secondary structure, extracts structural motifs, and searches the database for similar secondary structure motifs and interacting small molecule. We demonstrated the utility of the server by querying α-synuclein mRNA 5' UTR sequence and finding potential matches which were validated as correct. The server is publicly available at http://RNALigands.ccbr.utoronto.ca The source code can also be downloaded at https://github.com/SaisaiSun/RNALigands.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.