Extend-NMR: Extending NMR for Functional and Structural Genomics
Partner 2:European Bioinformatics Institute
People involved:Chris Penkett, Wim Vranken & Kim Henrick

Deposition: To PDB and BMRB from a CCPN project.

The work within Extend-NMR on the large scale analysis of constraint and chemical shift data shows again how important it is for scientists to deposit their data consistently and correctly. The final step in the Extend-NMR pipeline is therefore deposition of the final data in the CCPN project to the wwPDB and the BMRB: this is now possible due to an extension of the Autodep software at the PDBe.

The CcpNmr ECI is the final step in the Extend-NMR pipeline: it allows the user to identify the final (ready for deposition) data and add information about authors, citations, ... . The CCPN project is then uploaded to the Autodep deposition server at the PDBe, where all information necessary for deposition to the wwPDB is extracted. After curation of the wwPDB deposition, any changes or additional data are fed back to the original CCPN project. It is then converted into NMR-STAR format and sent to the BMRB to make further deposition of NMR-related data possible.

Deposition features

  • Upload of CCPN project to Autodep for PDB deposition.
  • Automatic update of CCPN project after curation of data.
  • Forwarding of NMR-STAR file from CCPN project to BMRB.

Identifying final data for deposition using CcpNmr ECI
Upload and deposition of coordinates to PDB via Autodep
Further deposition of NMR data to BMRB