ArticleBioinformatics (Oxford, England)2025
DNAdesign: feature-aware in silico design of synthetic DNA through mutation.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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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.
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Who cites it
3 citing papers in PubMed.
- ShapeME: A Tool and Web Front-end for De Novo Discovery of Structural Motifs Underpinning Protein-DNA Interactions.Journal of molecular biology · 2026Article
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationDNA sequence and shape readout represent different modes of protein-DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.
resultsDNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all mutation candidates along the sequence and shape dimensions, with interactive visualization comparing each candidate with the wild-type DNA molecule. DNAdesign provides an approach to studying gene regulation and applications in synthetic biology, such as the design of synthetic enhancers and transcription factor binding sites. AVAILABILITY AND IMPLEMENTATION: The DNAdesign webserver and documentation are freely accessible at https://dnadesign.usc.edu.
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Registered trials
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