ArticleNucleic acids research2010
Computational generation and screening of RNA motifs in large nucleotide sequence pools.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- RaptScore: a large language model-based algorithm for versatile aptamer evaluation.Nucleic acids research · 2026Article
- Insulin Quantification Through Electrochemical and Optical Aptasensors: A Review.Annals of biomedical engineering · 2025Review
- RNA-EFM: energy-based flow matching for protein-conditioned RNA sequence-structure co-design.Bioinformatics advances · 2025Article
- AptaDiff: de novo design and optimization of aptamers based on diffusion models.Briefings in bioinformatics · 2024Article
- Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach.Molecules (Basel, Switzerland) · 2022Article
- Secondary Structure Libraries for Artificial Evolution Experiments.Molecules (Basel, Switzerland) · 2021Article
- In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.Nucleic acids research · 2017Article
- Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach.Journal of molecular biology · 2016Article
- New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization.Molecular therapy. Nucleic acids · 2014Article
- Graph-based sampling for approximating global helical topologies of RNA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- RNA graph partitioning for the discovery of RNA modularity: a novel application of graph partition algorithm to biology.PloS one · 2014Article
- Network Theory Tools for RNA Modeling.WSEAS transactions on mathematics · 2013Article
- Article
- Systematic evaluation of the dependence of deoxyribozyme catalysis on random region length.ACS combinatorial science · 2012Article
- Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function.PLoS computational biology · 2012Article
- Computational approaches to RNA structure prediction, analysis, and design.Current opinion in structural biology · 2011Review
- RAG: an update to the RNA-As-Graphs resource.BMC bioinformatics · 2011Article
- Computational approaches toward the design of pools for the in vitro selection of complex aptamers.RNA (New York, N.Y.) · 2010Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Although identification of active motifs in large random sequence pools is central to RNA in vitro selection, no systematic computational equivalent of this process has yet been developed. We develop a computational approach that combines target pool generation, motif scanning and motif screening using secondary structure analysis for applications to 10(12)-10(14)-sequence pools; large pool sizes are made possible using program redesign and supercomputing resources. We use the new protocol to search for aptamer and ribozyme motifs in pools up to experimental pool size (10(14) sequences). We show that motif scanning, structure matching and flanking sequence analysis, respectively, reduce the initial sequence pool by 6-8, 1-2 and 1 orders of magnitude, consistent with the rare occurrence of active motifs in random pools. The final yields match the theoretical yields from probability theory for simple motifs and overestimate experimental yields, which constitute lower bounds, for aptamers because screening analyses beyond secondary structure information are not considered systematically. We also show that designed pools using our nucleotide transition probability matrices can produce higher yields for RNA ligase motifs than random pools. Our methods for generating, analyzing and designing large pools can help improve RNA design via simulation of aspects of in vitro selection.
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