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NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

https://doi.org/10.1093/database/baw002
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Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

1 of the 31 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-11): 10.1073/pnas.1301810110 (notice 2017-08-30).

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/chem.201304053openalex-snapshot
From Intercalation to Groove Binding: Switching the DNA‐Binding Mode of Isostructural Transition‐Metal Complexes
inferredcites →https://doi.org/10.1007/s10822-014-9813-4openalex-snapshot
Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling
inferredcites →https://doi.org/10.1016/j.bbagrm.2015.06.010openalex-snapshot
Stressing out over long noncoding RNA
inferredcites →https://doi.org/10.1016/j.bpj.2012.10.029openalex-snapshot
Kinetics of the Triplex-Duplex Transition in DNA
inferredcites →https://doi.org/10.1016/j.dnarep.2015.04.017openalex-snapshot
RNA-directed repair of DNA double-strand breaks
inferredcites →https://doi.org/10.1016/j.ejmech.2014.03.061openalex-snapshot
Identification and optimization of novel Hsp90 inhibitors with tetrahydropyrido[4,3-d]pyrimidines core through shape-based screening
inferredcites →https://doi.org/10.1016/j.ymeth.2014.06.009openalex-snapshot
3D virtual screening of large combinatorial spaces
inferredcites →https://doi.org/10.1016/s0169-409x(00)00129-0openalex-snapshot
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1
inferredcites →https://doi.org/10.1021/bi00034a013openalex-snapshot
Relative Thermodynamic Stability of DNA, RNA, and DNA:RNA Hybrid Duplexes: Relationship with Base Composition and Structure
inferredcites →https://doi.org/10.1021/cb300135hopenalex-snapshot
A Small Molecule That Targets r(CGG)exp and Improves Defects in Fragile X-Associated Tremor Ataxia Syndrome
inferredcites →https://doi.org/10.1021/ci5004703openalex-snapshot
Design of Novel Rho Kinase Inhibitors Using Energy Based Pharmacophore Modeling, Shape-Based Screening, in Silico Virtual Screening, and Biological Evaluation
inferredcites →https://doi.org/10.1021/ci800339popenalex-snapshot
Simple Idea to Generate Fragment and Pharmacophore Descriptors and Their Implications in Chemical Informatics
inferredcites →https://doi.org/10.1021/jp411280nopenalex-snapshot
Conformational Dynamics of DNA Hairpins at Millisecond Resolution Obtained from Analysis of Single-Molecule FRET Histograms
inferredcites →https://doi.org/10.1038/srep01016openalex-snapshot
C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms RNA G-quadruplexes
inferredcites →https://doi.org/10.1039/c4ra14553dopenalex-snapshot
Exploring the mode of binding of the bioflavonoid kaempferol with B and protonated forms of DNA using spectroscopic and molecular docking studies
inferredcites →https://doi.org/10.1039/c5cc01678aopenalex-snapshot
Small molecule binding to a G-hairpin and a G-triplex: a new insight into anticancer drug design targeting G-rich regions
inferredcites →https://doi.org/10.1042/bj20141063openalex-snapshot
A stable RNA G-quadruplex within the 5′-UTR of Arabidopsis thaliana ATR mRNA inhibits translation
inferredcites →https://doi.org/10.1073/pnas.1301810110openalex-snapshot
RETRACTED: Somatic hypermutation maintains antibody thermodynamic stability during affinity maturation
inferredcites →https://doi.org/10.1074/jbc.c113.502336openalex-snapshot
TMPyP4 Porphyrin Distorts RNA G-quadruplex Structures of the Disease-associated r(GGGGCC)n Repeat of the C9orf72 Gene and Blocks Interaction of RNA-binding Proteins
inferredcites →https://doi.org/10.1080/07391102.2012.687518openalex-snapshot
Coexistence of G-quadruplex and duplex domains within the secondary structure of 31-mer DNA thrombin-binding aptamer
inferredcites →https://doi.org/10.1080/07391102.2013.872052openalex-snapshot
3D-QSAR studies and shape based virtual screening for identification of novel hits to inhibit MbtA inMycobacterium tuberculosis
inferredcites →https://doi.org/10.1080/07391102.2014.929535openalex-snapshot
Shape-based virtual screening, docking, and molecular dynamics simulations to identifyMtb-ASADH inhibitors
inferredcites →https://doi.org/10.1088/1478-3975/8/6/066006openalex-snapshot
Quantitative analysis of the ion-dependent folding stability of DNA triplexes
inferredcites →https://doi.org/10.1093/jxb/erv312openalex-snapshot
Salt-induced transcription factor MYB74 is regulated by the RNA-directed DNA methylation pathway in Arabidopsis
inferredcites →https://doi.org/10.1093/nar/gki869openalex-snapshot
Characterization of the bisintercalative DNA binding mode of a bifunctional platinum-acridine agent
inferredcites →https://doi.org/10.1093/nar/gks1101openalex-snapshot
G4LDB: a database for discovering and studying G-quadruplex ligands
inferredcites →https://doi.org/10.1093/nar/gkt976openalex-snapshot
SMMRNA: a database of small molecule modulators of RNA
inferredcites →https://doi.org/10.1111/cbdd.12432openalex-snapshot
Discovery of New Non‐Steroidal F arnesoid X R eceptor Modulators Through 3 D Shape Similarity Search and Structure‐Based Virtual Screening
inferredcites →https://doi.org/10.1140/epje/i2013-13057-4openalex-snapshot
DNA triplex folding: Moderate versus high salt conditions
inferredcites →https://doi.org/10.3389/fgene.2015.00209openalex-snapshot
Replication of Structured DNA and its implication in epigenetic stability
inferredcites →https://doi.org/10.3390/biom5020943openalex-snapshot
RNA-Mediated Regulation of HMGA1 Function

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/9783527840458.ch13openalex-snapshot
Outlook
inferred← citeshttps://doi.org/10.1002/9783527840458.ch5openalex-snapshot
Chemical Matter That Binds RNA
inferred← citeshttps://doi.org/10.1002/ange.201707641openalex-snapshot
Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA‐Targeted Bioactive Ligands
inferred← citeshttps://doi.org/10.1002/ange.202211358openalex-snapshot
Machine Learning Informs RNA‐Binding Chemical Space**
inferred← citeshttps://doi.org/10.1002/anie.201707641openalex-snapshot
Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA‐Targeted Bioactive Ligands
inferred← citeshttps://doi.org/10.1002/anie.202211358openalex-snapshot
Machine Learning Informs RNA‐Binding Chemical Space**
inferred← citeshttps://doi.org/10.1007/s00604-018-2903-6openalex-snapshot
Highly sensitive fluorometric determination of thrombin by on-chip signal amplification initiated by terminal deoxynucleotidyl transferase
inferred← citeshttps://doi.org/10.1016/j.aichem.2024.100053openalex-snapshot
Advances in machine-learning approaches to RNA-targeted drug design
inferred← citeshttps://doi.org/10.1016/j.drudis.2025.104366openalex-snapshot
Artificial intelligence for RNA–ligand interaction prediction: advances and prospects
inferred← citeshttps://doi.org/10.1016/j.ejmech.2026.118795openalex-snapshot
PRISM: A structure-guided computational approach for identifying RNA-targeting small molecules by integrating 3D conformational and chemical information
inferred← citeshttps://doi.org/10.1016/j.jmb.2022.167914openalex-snapshot
R-SIM: A Database of Binding Affinities for RNA-small Molecule Interactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00155openalex-snapshot
DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00152openalex-snapshot
Evaluating Molecular Docking Programs for RNA-Targeted Ligand Screening: Influence of Binding Modes and Ligand Types
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00381openalex-snapshot
SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c00973openalex-snapshot
Advances and Challenges in Machine Learning for RNA-Small Molecule Interaction Modeling: Review
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c01854openalex-snapshot
Halogen Bonds Exist between Noncovalent Ligands and Natural Nucleic Acids
inferred← citeshttps://doi.org/10.1021/acschembio.9b00631openalex-snapshot
R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes
inferred← citeshttps://doi.org/10.1038/s41467-024-49638-7openalex-snapshot
Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN
inferred← citeshttps://doi.org/10.1038/s41587-025-02942-zopenalex-snapshot
Predicting small molecule–RNA interactions without RNA tertiary structures
inferred← citeshttps://doi.org/10.1039/d4cb00287copenalex-snapshot
Three- and four-stranded nucleic acid structures and their ligands
inferred← citeshttps://doi.org/10.1080/1061186x.2017.1401076openalex-snapshot
Novel advances in targeted drug delivery
inferred← citeshttps://doi.org/10.1080/15476286.2023.2231708openalex-snapshot
Characterizing RNA-binding ligands on structures, chemical information, binding affinity and drug-likeness
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac483openalex-snapshot
HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design
inferred← citeshttps://doi.org/10.1093/nar/gkab952openalex-snapshot
G4LDB 2.2: a database for discovering and studying G-quadruplex and i-Motif ligands
inferred← citeshttps://doi.org/10.1093/nar/gkaf1016openalex-snapshot
Ribocentre-aptamer: an integrative, structure-focused database for RNA aptamers
inferred← citeshttps://doi.org/10.1177/2472555220922802openalex-snapshot
Target-Directed Approaches for Screening Small Molecules against RNA Targets
inferred← citeshttps://doi.org/10.1186/s12859-021-04349-4openalex-snapshot
RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources
inferred← citeshttps://doi.org/10.1261/rna.076257.120openalex-snapshot
Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem–loop RNAs and their implications for functional cellular assays
inferred← citeshttps://doi.org/10.2174/1568026619666190816101948openalex-snapshot
Virtual Screening Techniques in Drug Discovery: Review and Recent Applications
inferred← citeshttps://doi.org/10.26434/chemrxiv.13303187openalex-snapshot
DrugPred_RNA – Structure-Based Druggability Predictions for RNA Binding Sites
inferred← citeshttps://doi.org/10.26434/chemrxiv.13303187.v1openalex-snapshot
DrugPred_RNA – Structure-Based Druggability Predictions for RNA Binding Sites
inferred← citeshttps://doi.org/10.3390/ijms24065497openalex-snapshot
RPflex: A Coarse-Grained Network Model for RNA Pocket Flexibility Study
inferred← citeshttps://doi.org/10.3390/life15010104openalex-snapshot
Advances and Mechanisms of RNA–Ligand Interaction Predictions
inferred← citeshttps://doi.org/10.64898/2026.09.07.749797openalex-snapshot
HARIBOSS++: An Integrated Platform for RNA-Targeted Drug Design
inferred← citeshttps://doi.org/10.70675/f278a628z9cf1z4408za15fzfed05518864eopenalex-snapshot
Techniques computationnelles avancées pour aider la conception rationnelle de petites molécules ciblant l'ARN
inferred← citeshttps://doi.org/10.82308/26390openalex-snapshot
Computational evaluation of binding property of riboswitches and optimization of self-docking of RNA-ligand complexes for drug discovery
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