ArticleNucleic acids research2020
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- A comprehensive in silico investigation into the deleterious nonsynonymous single nucleotide polymorphisms of the human transcription factor EB (TFEB) gene and their predicted association with cancer.Journal, genetic engineering & biotechnology · 2026Article
- DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis.Nucleic acids research · 2026Article
- Multimodal bHLH-PAS DNA binding controls specificity and drives obesity.Nucleic acids research · 2026Article
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- The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation.Nucleic acids research · 2025Article
- Mechanistic understanding of UvrA damage detection and lesion hand-off to UvrB in Nucleotide Excision Repair.Nature communications · 2025Article
- Article
- Deciphering aptamer-protein interactions for bovine sperm sorting through in silico and in vitro studies.Molecular biology reports · 2025Article
- Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC.Nucleic acids research · 2025Article
- DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes.Nucleic acids research · 2025Article
- Bioinformatics Approaches for Understanding the Binding Affinity of Protein-Nucleic Acid Complexes.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis.Bioresources and bioprocessing · 2024Article
- Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface.Nucleic acids research · 2024Article
- PPI3D: a web server for searching, analyzing and modeling protein-protein, protein-peptide and protein-nucleic acid interactions.Nucleic acids research · 2024Article
- The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.Nucleic acids research · 2024Article
- A comprehensive in silico investigation into the pathogenic SNPs in the RTEL1 gene and their biological consequences.PloS one · 2024Article
- Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints.Nature communications · 2023Article
- Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays.Nature structural & molecular biology · 2023Article
- Polγ coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.Nature structural & molecular biology · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
DNAproDB (https://dnaprodb.usc.edu) is a web-based database and structural analysis tool that offers a combination of data visualization, data processing and search functionality that improves the speed and ease with which researchers can analyze, access and visualize structural data of DNA-protein complexes. In this paper, we report significant improvements made to DNAproDB since its initial release. DNAproDB now supports any DNA secondary structure from typical B-form DNA to single-stranded DNA to G-quadruplexes. We have updated the structure of our data files to support complex DNA conformations, multiple DNA-protein complexes within a DNAproDB entry and model indexing for analysis of ensemble data. Support for chemically modified residues and nucleotides has been significantly improved along with the addition of new structural features, improved structural moiety assignment and use of more sequence-based annotations. We have redesigned our report pages and search forms to support these enhancements, and the DNAproDB website has been improved to be more responsive and user-friendly. DNAproDB is now integrated with the Nucleic Acid Database, and we have increased our coverage of available Protein Data Bank entries. Our database now contains 95% of all available DNA-protein complexes, making our tools for analysis of these structures accessible to a broad community.
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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.