ReviewCurrent opinion in structural biology2009
Nuance in the double-helix and its role in protein-DNA recognition.
Review in Current opinion in structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
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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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed.
- DNA Wrapping by a tetrameric bacterial histone.Nature communications · 2025Article
- Adenovirus maturation establishes the transcription competent packaging of its genome.EMBO reports · 2025Article
- Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.Nucleic acids research · 2024Article
- The roles of DNA methylation on pH dependent i-motif (iM) formation in rice.Nucleic acids research · 2024Article
- Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics.Molecular therapy. Nucleic acids · 2023Article
- Insights into DNA solvation found in protein-DNA structures.Biophysical journal · 2022Review
- Structural basis for cell type specific DNA binding of C/EBPβ: The case of cell cycle inhibitor p15INK4b promoter.Journal of structural biology · 2022Article
- Article
- Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches.Biomolecules · 2022Review
- A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM).Nucleic acids research · 2022Article
- Genome information processing by the INO80 chromatin remodeler positions nucleosomes.Nature communications · 2021Article
- A perspective on the molecular simulation of DNA from structural and functional aspects.Chemical science · 2021Review
- Slow motions in A·T rich DNA sequence.Scientific reports · 2020Article
- Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.International journal of molecular sciences · 2020Article
- Post-translational modifications of Drosophila melanogaster HOX protein, Sex combs reduced.PloS one · 2020Article
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
- Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.Nucleic acids research · 2018Article
- Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins.Scientific reports · 2018Article
- SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site.Genome research · 2018Article
- Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.Nucleic acids research · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
It has been known for some time that the double-helix is not a uniform structure but rather exhibits sequence-specific variations that, combined with base-specific intermolecular interactions, offer the possibility of numerous modes of protein-DNA recognition. All-atom simulations have revealed mechanistic insights into the structural and energetic basis of various recognition mechanisms for a number of protein-DNA complexes while coarser grained simulations have begun to provide an understanding of the function of larger assemblies. Molecular simulations have also been applied to the prediction of transcription factor binding sites, while empirical approaches have been developed to predict nucleosome positioning. Studies that combine and integrate experimental, statistical and computational data offer the promise of rapid advances in our understanding of protein-DNA recognition mechanisms.
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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.