ArticleNucleic acids research2014
SMMRNA: a database of small molecule modulators of RNA.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
19 citing papers in PubMed.
- Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.Microorganisms · 2026Review
- Predicting small molecule-RNA interactions without RNA tertiary structures.Nature biotechnology · 2026Article
- Advances and Mechanisms of RNA-Ligand Interaction Predictions.Life (Basel, Switzerland) · 2025Review
- Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN.Nature communications · 2024Article
- 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
- Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning.Briefings in bioinformatics · 2024Article
- Identification and experimental validation of programmed cell death- and mitochondria-associated biomarkers in osteoporosis and immune microenvironment.Frontiers in genetics · 2024Article
- SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules.Journal of chemical theory and computation · 2022Article
- SMART v1.0: A Database for Small Molecules with Functional Implications in Plants.Interdisciplinary sciences, computational life sciences · 2022Article
- RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources.BMC bioinformatics · 2021Article
- DrugPred_RNA-A Tool for Structure-Based Druggability Predictions for RNA Binding Sites.Journal of chemical information and modeling · 2021Article
- Design of a small molecule that stimulates vascular endothelial growth factor A enabled by screening RNA fold-small molecule interactions.Nature chemistry · 2020Article
- Target-Directed Approaches for Screening Small Molecules against RNA Targets.SLAS discovery : advancing life sciences R & D · 2020Review
- R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes.ACS chemical biology · 2019Article
- SMMDB: a web-accessible database for small molecule modulators and their targets involved in neurological diseases.Database : the journal of biological databases and curation · 2018Article
- NALDB: nucleic acid ligand database for small molecules targeting nucleic acid.Database : the journal of biological databases and curation · 2016Article
- ONRLDB--manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery.Database : the journal of biological databases and curation · 2015Article
- EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape.Database : the journal of biological databases and curation · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed SMMRNA, an interactive database, available at http://www.smmrna.org, with special focus on small molecule ligands targeting RNA. Currently, SMMRNA consists of ∼770 unique ligands along with structural images of RNA molecules. Each ligand in the SMMRNA contains information such as Kd, Ki, IC50, ΔTm, molecular weight (MW), hydrogen donor and acceptor count, XlogP, number of rotatable bonds, number of aromatic rings and 2D and 3D structures. These parameters can be explored using text search, advanced search, substructure and similarity-based analysis tools that are embedded in SMMRNA. A structure editor is provided for 3D visualization of ligands. Advance analysis can be performed using substructure and OpenBabel-based chemical similarity fingerprints. Upload facility for both RNA and ligands is also provided. The physicochemical properties of the ligands were further examined using OpenBabel descriptors, hierarchical clustering, binning partition and multidimensional scaling. We have also generated a 3D conformation database of ligands to support the structure and ligand-based screening. SMMRNA provides comprehensive resource for further design, development and refinement of small molecule modulators for selective targeting of RNA molecules.
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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.