A worldwide e-Infrastructure for NMR and structural biology

CASD-NMR data deposit

For CASD-NMR data contributors

A blind data set will consist of:

  1. Text file including
    1. Name of Researcher
    2. Name of Laboratory
    3. Institution
    4. SwissProt ID of Protein
    5. Name of Protein from SwissProt
    6. Protein Sequence in FASTA format
    7. Biochemical information that was not obtained by NMR, such as oligomerization state, disulfide bonds, presence of metal ions/ligands bound to the protein, etc. (see also later)
    8. PDB ID
    9. Date of PDB Deposition
    10. Expected Date of PDB Release
       
  2. Chemical shift assignments in BioMagResDB 3.1 format. If your native data come in another format, please contact us and we will help with format conversion (alternatively check the tools available at the BMRB). Note that your chemical shift data may be re-referenced by us, on the basis of LACS output (more info here).
     
  3. Your final NOE peak lists, containing either peak volumes or heights (one list per each NOE experiment performed) preferably in BioMagResDB 3.1 format. If your native data come in another format, please contact us and we will help with format conversion (alternatively check the tools available at the BMRB). Please explicitly mention if the sample was in D2O, the isotope labeling scheme, and include sweep widths and carrier frequency (in ppm) in each frequency dimension.
     
  4. Optionally (preferably), the corresponding raw NOESY spectra (FIDs) as gzipped tar file(s).
     
  5. In the absence of 4., we would be grateful if you could provide us with an automatically peaked list.

 

What will we do with your data?

Your input data will be made available to the registered CASD-NMR participants via password-protected access (unless you want us to immediately deposit them in the public part of the site). After eight weeks, if the structure has not been released from the PDB yet, we will ask you to provide us with coordinates to enable comparisons with the CASD-NMR results. The coordinates will be made available only to the validators, i.e.the CING developers and the PSVS developers. No structural information (coordinates or images, including those generated by CASD-participants) will be made publicly available before your structure is released by the PDB. We may however disseminate numeric data from the CASD-NMR assessment such as Z-scores for the CASD-NMR results or RMSD values between the results and your reference structure.After your structure is released by the PDB, all experimental data and results will be moved to the public part of the CASD-NMR web site.
 

How to submit?

 
Please contact us by e-mail. We will then ask you to ftp all the materials above and will take care of distributing the data as described above.
 
 
Back to CASD-NMR home.
 
 

Biochemical information details

  • If the protein is a multimer, state if you provided X-filtered data
  • If metals or other cofactors are present, specify which atoms of the protein are the metal/cofactor ligands

 

Cite WeNMR

 
Usage of the WeNMR portals should be acknowledged in any publication:
 
"The WeNMR project (European FP7 e-Infrastructure grant, contract no. 261572www.wenmr.eu), supported by the European Grid Initiative (EGI) through the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan, the Latin America GRID infrastructure via the Gisela project, the International Desktop Grid Federation (IDGF) with its volunteers and the US Open Science Grid (OSG) are acknowledged for the use of web portals, computing and storage facilities. "
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572