ArticleNucleic acids research2020
RaptRanker: in silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Structure-guided engineering of an aptamer-PROTAC for targeted degradation of vaccinia-related kinase 1.Chemical science · 2026Article
- Advancements in Nanomaterial-Based Biosensors for Neuropsychiatric and Neurodegenerative Diagnostics: From Biomarker Discovery to Clinical Translation.Biosensors · 2026Review
- Review
- Are we there yet with XNA aptamers?RSC advances · 2026Review
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 2026Review
- De novo design of functional nucleic acids of aptamers.Nature computational science · 2026Article
- Nanomaterials-Based Electrochemical Aptasensors for Rapid Detection of Pathogens and By-Products.Molecules (Basel, Switzerland) · 2026Review
- Single-round evolution of RNA aptamers with GRAPE-LM.Nature biotechnology · 2026Article
- RaptScore: a large language model-based algorithm for versatile aptamer evaluation.Nucleic acids research · 2026Article
- From randomness to recognition: modeling the evolution of DNA sequence information during enrichment for binding.Bioinformatics advances · 2026Article
- Generation of RNA aptamers against chikungunya virus E2 envelope protein.Journal of virology · 2025Article
- DeepAptamer: Advancing high-affinity aptamer discovery with a hybrid deep learning model.Molecular therapy. Nucleic acids · 2025Article
- Landscape of small nucleic acid therapeutics: moving from the bench to the clinic as next-generation medicines.Signal transduction and targeted therapy · 2025Review
- AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.Molecular therapy. Nucleic acids · 2024Article
- A chimeric RNA consisting of siRNA and aptamer for inhibiting dengue virus replication.NAR molecular medicine · 2024Article
- Review
- RaptGen-Assisted Generation of an RNA/DNA Hybrid Aptamer against SARS-CoV-2 Spike Protein.Biochemistry · 2024Article
- Aptamers as an approach to targeted cancer therapy.Cancer cell international · 2024Review
- Diagnostic and Therapeutic Aptamers: A Promising Pathway to Improved Cardiovascular Disease Management.JACC. Basic to translational science · 2024Review
- Aptamers in neuro-oncology: An emerging therapeutic modality.Neuro-oncology · 2024Review
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7 authors.
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Abstract
Aptamers are short single-stranded RNA/DNA molecules that bind to specific target molecules. Aptamers with high binding-affinity and target specificity are identified using an in vitro procedure called high throughput systematic evolution of ligands by exponential enrichment (HT-SELEX). However, the development of aptamer affinity reagents takes a considerable amount of time and is costly because HT-SELEX produces a large dataset of candidate sequences, some of which have insufficient binding-affinity. Here, we present RNA aptamer Ranker (RaptRanker), a novel in silico method for identifying high binding-affinity aptamers from HT-SELEX data by scoring and ranking. RaptRanker analyzes HT-SELEX data by evaluating the nucleotide sequence and secondary structure simultaneously, and by ranking according to scores reflecting local structure and sequence frequencies. To evaluate the performance of RaptRanker, we performed two new HT-SELEX experiments, and evaluated binding affinities of a part of sequences that include aptamers with low binding-affinity. In both datasets, the performance of RaptRanker was superior to Frequency, Enrichment and MPBind. We also confirmed that the consideration of secondary structures is effective in HT-SELEX data analysis, and that RaptRanker successfully predicted the essential subsequence motifs in each identified sequence.
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