Getting Started with DNAproDB

DNAproDB is a database and web-based visualization tool which is intended to make structural analysis of DNA-Protein complexes easy. Here you'll find a wealth of data on the structure of and interaction between DNA and proteins in complex for structures contained in the PDB. This data can be used to analyze individual structures, or to generate large datasets by constructing queries on a set of structural and interaction features using the search form. Additionally, you can upload your own structure using the upload form, and use the same processing and visualization tools for unpublished data.

The data you retrieve can be downloaded directly for your use, or can be visualized with our built-in visualization tools. Use the navigation bar at the top of the page to explore different areas of the site. Full documentation is available at the documentation page.

If you use DNAproDB in your work, please cite us: Jared M. Sagendorf, Helen M. Berman, Remo Rohs; DNAproDB: an interactive tool for structural analysis of DNA–protein complexes. Nucleic Acids Res 2017, 45, W89-W97. doi: 10.1093/nar/gkx272

The DNAproDB database

Latest PDB Data Retrieval:

Latest DNAproDB Update:

DNAproDB provides data on structures from the PDB which contain at least one protein bound to a helical region of double-stranded DNA. Large structures (Molecular weight > 201000), structures with less than five base pairs and structures with more than one helical region of DNA are currently not included.

The data is organized in a hierarchical manner. The diagram below gives an overview of the way the data is organized and stored in the database. The same data hierarchy applies to uploaded structures as well.

The structure may contain multiple proteins in complex with a helical region of DNA and all information contained and generated from a single structure file is stored as a single entity in the database, or a single JSON file for uploaded structures.
Information that is exclusive to the DNA contained in the structure file.

    Sequence Features

  • Bound Sequence
  • GC Content
  • A-tracts
  • ...and more
  • Structural Features

  • Base Pairing
  • Non Watson-Crick Base Pairing
  • Helical Geometry
  • Shape Parameters (Inter-BP, Intra-BP, Groove width)
  • DNA Form (A, B, Z, Other)
  • Solvent Accessibility
  • ...and more
Information related to the interactions between DNA and protein.

Pairwise Nucleotide-Residue interactions

  • Hydrogen bonding
  • VdW interactions
  • Interaction geometry
  • Contact BASA
  • ...and more

Global Interaction Properties

  • Interface SS Composition
  • Residue Propensity
  • Groove Contacts
  • ...and more
Information that is exclusive to the protein(s) contained in the structure file

    Chain Features

  • Sequences
  • Secondary Structure
  • CATH Classification
  • BLAST Sequence Clusters
  • UniProt Name and IDs
  • ...and more
  • SSE Features

  • SSE Identification
  • Assigned Axial Coordinates
  • Child Residues
  • Nucleotide Interactions
  • ...and more
  • Residue Features

  • Solvent Accessibility
  • SAP Score
  • Chemical Modifications
  • ...and more

Creating Visualizations

When viewing a report for an individual structure, you'll be presented with several interactive charts wich are linked to a three-dimensional view of the complex. Clicking on the various secondary structural elements (SSE) will highlight them in the 3D view, and hovering over elements in the charts will display additional information.