ArticleNucleic acids research2017
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 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.
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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
46 citing papers in PubMed.
- Molecular dynamics and evolutionary conservation of FUL-SOC1 regulatory interactions in polyploid Brassica juncea.Functional & integrative genomics · 2026Article
- The Kaposi's sarcoma-associated herpesvirus TBP mimic uses a noncanonical DNA-binding mode to promote viral late gene transcription.Nucleic acids research · 2025Article
- Mechanistic understanding of UvrA damage detection and lesion hand-off to UvrB in Nucleotide Excision Repair.Nature communications · 2025Article
- Multiple combinatorial interactions among natural structural variants of Brassica SOC1 promoters and SVP: conservation of binding affinity despite diversity in bimolecular interactions.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
- Article
- Characterization of argonaute nucleases from mesophilic bacteria Pseudobutyrivibrio ruminis.Bioresources and bioprocessing · 2024Article
- Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element.Structure (London, England : 1993) · 2024Article
- Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface.Nucleic acids research · 2024Article
- A comprehensive in silico investigation into the pathogenic SNPs in the RTEL1 gene and their biological consequences.PloS one · 2024Article
- Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment.PLoS computational biology · 2023Article
- Replication fork binding triggers structural changes in the PriA helicase that govern DNA replication restart in E. coli.Nature communications · 2023Article
- Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions.BMC molecular and cell biology · 2023Article
- Article
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- Developing Community Resources for Nucleic Acid Structures.Life (Basel, Switzerland) · 2022Review
- Pretransition state and apo structures of the filament-forming enzyme SgrAI elucidate mechanisms of activation and substrate specificity.The Journal of biological chemistry · 2022Article
- ProDFace: A web-tool for the dissection of protein-DNA interfaces.Frontiers in molecular biosciences · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA-protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA-protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA-protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA-protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA-protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu.
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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.