ArticleNucleic acids research2025
DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 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
- Crystal structure of the NKX2-1 homeodomain bound to a palindromic DNA recognition sequence.Acta crystallographica. Section F, Structural biology communications · 2026Article
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- R3DCID: circular interaction diagrams for RNA and DNA 3D structures of all sizes.RNA (New York, N.Y.) · 2026Article
- Mapping DNA glycosylase binding across lesion sequence contexts reveals extended sequence and structural recognition logic.Nature communications · 2026Article
- C620Y Mutation-Induced Destabilization of the Androgen Receptor Disrupts DNA Recognition Specificity in Prostate Cancer: Insights from Extensive Parametric Normal Mode Simulations.Cell biochemistry and biophysics · 2026Article
- Article
- Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site.Science advances · 2026Article
- ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces.Computational and structural biotechnology journal · 2026Article
- Article
- Computational design of sequence-specific DNA-binding proteins.Nature structural & molecular biology · 2025Article
- The Kaposi's sarcoma-associated herpesvirus TBP mimic uses a noncanonical DNA-binding mode to promote viral late gene transcription.Nucleic acids research · 2025Article
- Novel fold and wing structure of Forkhead transcription factor facilitate DNA binding.Nucleic acids research · 2025Article
- PInteract: Detecting Aromatic-Involving Motifs in Proteins and Protein-Nucleic Acid Complexes.Biomolecules · 2025Article
- Article
- Elucidating the role of mycobacteriophage D29-encoded Gp36 in DNA binding and phage gene expression regulation.Nucleic acids research · 2025Article
- AlphaFold 3-Assisted Deciphering of the DNA Recognition by DREB1 Transcription Factors in Rice.International journal of molecular sciences · 2025Article
- Article
- An archaeal nucleoid-associated protein binds an essential motif in DNA replication origins.Nature communications · 2025Article
- PARP2 Catalytic Activity Is Allosterically Stimulated by Binding to the c-KIT1 G-Quadruplex.ACS omega · 2025Article
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Authors and funding
5 authors.
Funding
Abstract
DNAproDB (https://dnaprodb.usc.edu/) is a database, visualization tool, and processing pipeline for analyzing structural features of protein-DNA interactions. Here, we present a substantially updated version of the database through additional structural annotations, search, and user interface functionalities. The update expands the number of pre-analyzed protein-DNA structures, which are automatically updated weekly. The analysis pipeline identifies water-mediated hydrogen bonds that are incorporated into the visualizations of protein-DNA complexes. Tertiary structure-aware nucleotide layouts are now available. New file formats and external database annotations are supported. The website has been redesigned, and interacting with graphs and data is more intuitive. We also present a statistical analysis on the updated collection of structures revealing salient patterns in protein-DNA interactions.
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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.