ArticleACS medicinal chemistry letters2011
Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids.
Article in ACS medicinal chemistry letters, 2011. 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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Who cites it
18 citing papers in PubMed.
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- Review
- SPRank─A Knowledge-Based Scoring Function for RNA-Ligand Pose Prediction and Virtual Screening.Journal of chemical theory and computation · 2024Article
- Advances in machine-learning approaches to RNA-targeted drug design.Artificial intelligence chemistry · 2024Article
- RLDOCK method for predicting RNA-small molecule binding modes.Methods (San Diego, Calif.) · 2022Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- Targeting structural features of viral genomes with a nano-sized supramolecular drug.Chemical science · 2021Article
- RLDOCK: A New Method for Predicting RNA-Ligand Interactions.Journal of chemical theory and computation · 2020Article
- Article
- How 'Protein-Docking' Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids?Molecules (Basel, Switzerland) · 2020Review
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- Small molecule compounds targeting miRNAs for cancer therapy.Advanced drug delivery reviews · 2015Review
- DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.PloS one · 2014Article
- Computational approaches to predicting the impact of novel bases on RNA structure and stability.ACS chemical biology · 2013Review
- Induced fit docking, and the use of QM/MM methods in docking.Drug discovery today. Technologies · 2013Review
- A combination of receptor-based pharmacophore modeling & QM techniques for identification of human chymase inhibitors.PloS one · 2013Article
- Novel insights of structure-based modeling for RNA-targeted drug discovery.Journal of chemical information and modeling · 2012Article
- RNA-ligand molecular docking: advances and challenges.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The highly flexible nature of RNA provides a formidable challenge for structure-based drug design approaches that target RNA. We introduce an approach for modeling target conformational changes in RNA-ligand docking based on potential grids that are represented as elastic bodies using Navier's equation. This representation provides an accurate and efficient description of RNA-ligand interactions even in the case of a moving RNA structure. When applied to a data set of 17 RNA-ligand complexes, filtered out of the largest validation data set used for RNA-ligand docking so far, the approach is twice as successful as docking into an apo structure and still half as successful as redocking to the holo structure. The approach allows considering RNA movements of up to 6 Å rmsd and is based on a uniform and robust parametrization of the properties of the elastic potential grids, so that the approach is applicable to different RNA-ligand complex classes.
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