ArticleNature communications2024
Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed.
- In silico designing of small molecules for targeting RNA: current landscape and future directions.Journal of computer-aided molecular design · 2026Review
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.Nucleic acids research · 2026Article
- Multiscale Modeling of the Bacterial Ribosome to Identify Potential Peptide Modulators and Their Allosteric Effects.Biochemistry · 2026Article
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- Designing small molecules targeting a cryptic RNA binding site through base displacement.Nature chemical biology · 2026Article
- RBM45 Preferential Binding to mThe journal of physical chemistry. B · 2026Article
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- A multi-stage computational pipeline andRSC advances · 2026Article
- Functional characterization of dynamic nascent RNA folding ensembles in real time.Science advances · 2026Article
- Making PLUMED Fly: A Tutorial on Optimizing Performance.The journal of physical chemistry. B · 2026Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- RNA language model and graph attention network for RNA and small molecule binding sites prediction.Bioinformatics (Oxford, England) · 2025Article
- MVRBind: multi-view learning for RNA-small molecule binding site prediction.Briefings in bioinformatics · 2025Article
- Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands.Angewandte Chemie (International ed. in English) · 2025Article
- Ligand-binding pockets in RNA and where to find them.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning.Nature communications · 2025Article
- Promotion of TLR7-MyD88-dependent inflammation and autoimmunity in mice through stem-loop changes in Lnc-Atg16l1.Nature communications · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The rational targeting of RNA with small molecules is hampered by our still limited understanding of RNA structural and dynamic properties. Most in silico tools for binding site identification rely on static structures and therefore cannot face the challenges posed by the dynamic nature of RNA molecules. Here, we present SHAMAN, a computational technique to identify potential small-molecule binding sites in RNA structural ensembles. SHAMAN enables exploring the conformational landscape of RNA with atomistic molecular dynamics simulations and at the same time identifying RNA pockets in an efficient way with the aid of probes and enhanced-sampling techniques. In our benchmark composed of large, structured riboswitches as well as small, flexible viral RNAs, SHAMAN successfully identifies all the experimentally resolved pockets and ranks them among the most favorite probe hotspots. Overall, SHAMAN sets a solid foundation for future drug design efforts targeting RNA with small molecules, effectively addressing the long-standing challenges in the field.
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Registered trials
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