ArticleWiley interdisciplinary reviews. Computational molecular science
RNA-ligand molecular docking: advances and challenges.
Article in Wiley interdisciplinary reviews. Computational molecular science. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 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
- Integrative in silico and in vitro screening of small molecules targeting RNA.Current protocols · 2026Article
- Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking.Journal of chemical information and modeling · 2026Article
- A multi-stage computational pipeline andRSC advances · 2026Article
- Article
- Therapeutic rewiring of ceRNA networks: a computational pipeline for drug repurposing in acute kidney injury via circRNA-miRNA-mRNA axis disruption.Human genomics · 2026Review
- Article
- Predicting small molecule-RNA interactions without RNA tertiary structures.Nature biotechnology · 2026Article
- MicroRNA-phytochemical interactome targeting thioredoxin-interacting protein: a narrative review at the nexus of RNA therapeutics, cancer biology, and metabolic regulation.Frontiers in oncology · 2026Review
- RNA-Targeted Therapeutics for Lipid Metabolic Disorders: From Bench to Bedside.Research (Washington, D.C.) · 2026Article
- Integrated Machine Learning and Structure-Based Virtual Screening Identifies Natural Product Targeting 50S Ribosome Inhibitory Activity AgainstMolecules (Basel, Switzerland) · 2025Article
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input.bioRxiv : the preprint server for biology · 2025Article
- Review
- Overcoming translational barriers in RNA-protein docking: enhancing computational accuracy for targeted drug discovery.Future medicinal chemistry · 2025Review
- Explainable Synthesizability Prediction of Inorganic Crystal Polymorphs Using Large Language Models.Angewandte Chemie (International ed. in English) · 2025Article
- Expanded ensemble predictions of toluene-water partition coefficients in the SAMPL9 logPhysical chemistry chemical physics : PCCP · 2025Article
- Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer.Journal of chemical information and modeling · 2025Article
- Novel target identification towards drug repurposing based on biological activity profiles.PloS one · 2025Article
- A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.Biophysics and physicobiology · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
With rapid advances in computer algorithms and hardware, fast and accurate virtual screening has led to a drastic acceleration in selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions has become an indispensable tool for RNA-targeted drug discovery. The current models for RNA-ligand binding have mainly focused on the docking-and-scoring method. Accurate docking and scoring should tackle four crucial problems: (1) conformational flexibility of ligand, (2) conformational flexibility of RNA, (3) efficient sampling of binding sites and binding poses, and (4) accurate scoring of different binding modes. Moreover, compared with the problem of protein-ligand docking, predicting ligand binding to RNA, a negatively charged polymer, is further complicated by additional effects such as metal ion effects. Thermodynamic models based on physics-based and knowledge-based scoring functions have shown highly encouraging success in predicting ligand binding poses and binding affinities. Recently, kinetic models for ligand binding have further suggested that including dissociation kinetics (residence time) in ligand docking would result in improved performance in estimating
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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.