ArticleACS chemical biology2019
R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes.
Article in ACS chemical biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 86 citations in OpenAlex.
- Structural Pockets and Interacting RNA-Associated Ligands (SPIRAL): A DSSR-enabled Meta-Analysis of RNA-Small Molecule Recognition.bioRxiv : the preprint server for biology · 2026Article
- AI-Augmented Iterative Screening of Libraries Against RNA Targets (AISLAR) Boosts Discovery of SAR-Tractable RNA Binders and Rational Analog Design.Small science · 2026Article
- NMR-Based Fragment Screening for RNA-Targeted Drug Discovery.Molecules (Basel, Switzerland) · 2026Review
- The kinase inhibitor palbociclib binds to HIV TAR RNA with very low nanomolar affinity and exquisite specificity.Nucleic acids research · 2026Article
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- Predicting small molecule-RNA interactions without RNA tertiary structures.Nature biotechnology · 2026Article
- Molecular insights into de novo small-molecule recognition by an intron RNA structure.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Harnessing Computational Approaches for RNA-Targeted Drug Discovery.RNA nanomed · 2024Article
- Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning.Briefings in bioinformatics · 2024Article
- Stereoselective RNA reaction with chiral 2'-OH acylating agents.Chemical science · 2023Article
- Pervasive transcriptome interactions of protein-targeted drugs.Nature chemistry · 2023Article
- New Xanthone Derivatives as Potent G-Quadruplex Binders for Developing Anti-Cancer Therapeutics.ACS pharmacology & translational science · 2023Article
- 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
- Machine Learning Informs RNA-Binding Chemical Space.Angewandte Chemie (International ed. in English) · 2023Article
- Characterizing RNA-binding ligands on structures, chemical information, binding affinity and drug-likeness.RNA biology · 2023Article
- A toolkit for the identification of NEAT1_2/paraspeckle modulators.Nucleic acids research · 2022Article
- In Silico Methods for Identification of Potential Active Sites of Therapeutic Targets.Molecules (Basel, Switzerland) · 2022Review
- SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules.Journal of chemical theory and computation · 2022Article
- Article
- 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
7 authors at 5 institutions in 1 country.
Funding
Abstract
While the opportunities available for targeting RNA with small molecules have been widely appreciated, the challenges associated with achieving specific RNA recognition in biological systems have hindered progress and prevented many researchers from entering the field. To facilitate the discovery of RNA-targeted chemical probes and their subsequent applications, we curated the RNA-targeted BIoactive ligaNd Database (R-BIND). This collection contains an array of information on reported chemical probes that target non-rRNA and have biological activity, and analysis has led to the discovery of RNA-privileged properties. Herein, we developed an online platform to make this information freely available to the community, offering search options, a suite of tools for probe development, and an updated R-BIND data set with detailed experimental information for each probe. We repeated the previous cheminformatics analysis on the updated R-BIND list and found that the distinguishing physicochemical, structural, and spatial properties remained unchanged, despite an almost 50% increase in the database size. Further, we developed several user-friendly tools, including queries based on cheminformatic parameters, experimental details, functional groups, and substructures. In addition, a nearest neighbor algorithm can assess the similarity of user-uploaded molecules to R-BIND ligands. These tools and resources can be used to design small molecule libraries, optimize lead ligands, or select targets, probes, assays, and control experiments. Chemical probes are critical to the study and discovery of novel functions for RNA, and we expect this resource to greatly assist researchers in exploring and developing successful RNA-targeted probes.
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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.