wwPDB OneDep System

Overview

The wwPDB partners have joined forces in creating the next generation of PDB deposition and annotation tools, OneDep. This system created to enhance the wwPDB's ability to meet the evolving deposition requirements from the scientific community over the next decade. The system unifies the deposition and annotation systems across all wwPDB deposition centers and focuses on improving data quality and completeness in the PDB archive, while supporting growth in the number of depositions and increases in size and complexity of the structures deposited.

wwPDB OneDep System

The latest version of the Deposition Tool interoperates with EMDB and BMRB to enable joint depositions of atomic coordinates (PDB) and electron density maps (EMDB) or NMR experimental data (BMRB). At the time of submission, PDB and EMDB/BMRB accession codes will be issued simultaneously.

Features

Deposition

  • A common, web-based deposition interface across all wwPDB sites
  • Minimization of manual entry. The new system easily extracts all information contained in PDBx/mmCIF depositions & pdb_extract output. A PDBx/mmCIF preparation guide is available
  • Submissions can be based on existing depositions
  • Enables coordinate and experimental data file replacement prior to submission and after processing
  • Preview and download PDB files post-submission
  • Supports structures determined by multiple methods that are currently accepted, i.e., X-ray/neutron hybrid method
  • PDBx/mmCIF is the master file format: The new system will accept, process, and distribute data in PDBx/mmCIF format.
  • Validation based on recommendations from community Task Forces (X-ray | EM | NMR)
  • Improved checking for ligand chemistry and polymer sequence consistency
  • Communicate with PDB annotation staff using web-based interface

Annotation

  • Validation Module
    • Based on recommendations from method-specific community Task Forces
      (X-ray | EM | NMR)
    • Creates PDF validation report for depositor review and submission to journals
      • Model quality, Model/data fit, Residue plots
      • Slider plots of key statistics for overall quality at-a-glance
      • Tabulations of diagnostics for entry components such as Macromolecules and Ligands
    • Summary table for key data and refinement stats
  • Improved status tracking and file versioning
  • Improve interface for 2D and 3D view in ligand chemistry comparison and sequence alignment
  • Calculated Annotations
    • Automatically derives data for secondary structure, binding sites, linkage and predicted biological assemblies are displayed in a tabular form at UI and 3D visualization for review and edit as needed