ArticleScientific reports2015
Rsite: a computational method to identify the functional sites of noncoding RNAs.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 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
- Machine Learning for RNA-Targeting Drug Design.Journal of chemical information and modeling · 2026Review
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- CoBRA: compound binding site prediction using RNA language model.Briefings in bioinformatics · 2026Article
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- DistRMI: a deep distance-aware neural network for explainable RNA loop motif-small molecule interaction prediction.Briefings in bioinformatics · 2025Article
- Advances in Methods for Accurate Prediction of RNA-Small Molecule Binding Sites: From Isolated to AI-Integrated Strategies.Pharmaceuticals (Basel, Switzerland) · 2025Review
- RNA language model and graph attention network for RNA and small molecule binding sites prediction.Bioinformatics (Oxford, England) · 2025Article
- Review
- MVRBind: multi-view learning for RNA-small molecule binding site prediction.Briefings in bioinformatics · 2025Article
- Advances and Mechanisms of RNA-Ligand Interaction Predictions.Life (Basel, Switzerland) · 2025Review
- AI-integrated network for RNA complex structure and dynamic prediction.Biophysics reviews · 2024Review
- Advances in machine-learning approaches to RNA-targeted drug design.Artificial intelligence chemistry · 2024Article
- Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction.Bioinformatics (Oxford, England) · 2024Article
- RNet: a network strategy to predict RNA binding preferences.Briefings in bioinformatics · 2023Article
- Dissecting and predicting different types of binding sites in nucleic acids based on structural information.Briefings in bioinformatics · 2022Article
- Structure-based deep learning for binding site detection in nucleic acid macromolecules.NAR genomics and bioinformatics · 2021Article
- Mining for Ligandable Cavities in RNA.ACS medicinal chemistry letters · 2021Article
- RBinds: A user-friendly server for RNA binding site prediction.Computational and structural biotechnology journal · 2020Article
- Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs.Scientific reports · 2016Article
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Authors and funding
4 authors.
Funding
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Abstract
There is an increasing demand for identifying the functional sites of noncoding RNAs (ncRNAs). Here we introduce a tertiary-structure based computational approach, Rsite, which first calculates the Euclidean distances between each nucleotide and all the other nucleotides in a RNA molecule and then determines the nucleotides that are the extreme points in the distance curve as the functional sites. By analyzing two ncRNAs, tRNA (Lys) and Diels-Alder ribozyme, we demonstrated the efficiency of Rsite. As a result, Rsite recognized all of the known functional sites of the two ncRNAs, suggesting that Rsite could be a potentially useful tool for discovering the functional sites of ncRNAs. The source codes and data sets of Rsite are available at http://www.cuilab.cn/rsite.
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