ArticleChemistry & biology2011
Novel ligands for a purine riboswitch discovered by RNA-ligand docking.
Article in Chemistry & biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- 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
- Engineering ligands for theophylline riboswitches expands its regulatory dynamic range in prokaryotic and eukaryotic systems.Nature communications · 2026Article
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- Discovery of RNA-Reactive Small Molecules Guides the Design of Electrophilic Modules for RNA-Specific Covalent Binders.Journal of the American Chemical Society · 2025Article
- Harnessing Computational Approaches for RNA-Targeted Drug Discovery.RNA nanomed · 2024Article
- Emerging Roles of ncRNAs in Type 2 Diabetes Mellitus: From Mechanisms to Drug Discovery.Biomolecules · 2024Review
- SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening.Journal of chemical theory and computation · 2024Article
- Structure-based virtual screening of unbiased and RNA-focused libraries to identify new ligands for the HCV IRES model system.RSC medicinal chemistry · 2024Article
- Article
- Fragment-Based Approaches to Identify RNA Binders.Journal of medicinal chemistry · 2023Review
- RNA 3D Modeling with FARFAR2, Online.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Low-Molecular Weight Small Molecules Can Potently Bind RNA and Affect Oncogenic Pathways in Cells.Journal of the American Chemical Society · 2022Article
- Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy.Journal of chemical information and modeling · 2021Article
- Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.PLoS computational biology · 2021Article
- RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources.BMC bioinformatics · 2021Article
- Mining for Ligandable Cavities in RNA.ACS medicinal chemistry letters · 2021Article
- Riboswitches as Drug Targets for Antibiotics.Antibiotics (Basel, Switzerland) · 2021Review
- RLDOCK: A New Method for Predicting RNA-Ligand Interactions.Journal of chemical theory and computation · 2020Article
- Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design.Cell chemical biology · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The increasing number of RNA crystal structures enables a structure-based approach to the discovery of new RNA-binding ligands. To develop the poorly explored area of RNA-ligand docking, we have conducted a virtual screening exercise for a purine riboswitch to probe the strengths and weaknesses of RNA-ligand docking. Using a standard protein-ligand docking program with only minor modifications, four new ligands with binding affinities in the micromolar range were identified, including two compounds based on molecular scaffolds not resembling known ligands. RNA-ligand docking performed comparably to protein-ligand docking indicating that this approach is a promising option to explore the wealth of RNA structures for structure-based ligand design.
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Registered trials
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