ArticlePloS one2021
PFRED: A computational platform for siRNA and antisense oligonucleotides design.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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
28 citing papers in PubMed.
- Silencing with precision: In silico strategies for antisense oligonucleotide engineering.Molecular biology reports · 2026Review
- Artificial intelligence in biologic drug discovery: A review of methodological evolution and therapeutic applications.Acta pharmaceutica Sinica. B · 2026Review
- ClinASO: An open-source platform for rapid drug discovery of gapmer antisense oligonucleotides.Molecular therapy. Nucleic acids · 2026Article
- QStrain: an interactive platform for viral genome analysis and nucleic acid therapeutic design.BMC bioinformatics · 2026Article
- A splice-switching antisense oligonucleotide approach for pediatric genetic epilepsies.bioRxiv : the preprint server for biology · 2025Article
- ASOptimizer: optimizing chemical diversity of antisense oligonucleotides through deep learning.Nucleic acids research · 2025Article
- Personalized allele-specific antisense oligonucleotides for GNAO1-neurodevelopmental disorder.Molecular therapy. Nucleic acids · 2025Article
- A new level of RNA-based plant protection: dsRNAs designed from functionally characterized siRNAs highly effective against Cucumber mosaic virus.Nucleic acids research · 2025Article
- Review
- ASOG: AntiSense Oligonucleotide Generator.Computational and structural biotechnology journal · 2025Article
- Design and Preliminary Screen of Antisense Oligonucleotides.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Deep learning facilitates efficient optimization of antisense oligonucleotide drugs.Molecular therapy. Nucleic acids · 2024Article
- ASOptimizer: Optimizing antisense oligonucleotides through deep learning for IDO1 gene regulation.Molecular therapy. Nucleic acids · 2024Article
- Tribulations and future opportunities for artificial intelligence in precision medicine.Journal of translational medicine · 2024Review
- Bioinformatics Approaches in the Development of Antifungal Therapeutics and Vaccines.Current genomics · 2024Review
- Effective Antiviral Application of Antisense in Plants by Exploiting Accessible Sites in the Target RNA.International journal of molecular sciences · 2023Article
- An enhanced biophysical screening strategy to investigate the affinity of ASOs for their target RNA.RSC chemical biology · 2023Article
- RNA-Based Strategies for Cancer Therapy: In Silico Design and Evaluation of ASOs for Targeted Exon Skipping.International journal of molecular sciences · 2023Article
- Ensemble-Learning and Feature Selection Techniques for Enhanced Antisense Oligonucleotide Efficacy Prediction in Exon Skipping.Pharmaceutics · 2023Article
- Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server.RNA (New York, N.Y.) · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred/pfred-gui/releases/tag/v1.0 as a java Jar file. The source code and the links for downloading the precompiled version can be found at https://github.com/pfred.
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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.