A worldwide e-Infrastructure for NMR and structural biology

CASD-NMR structure deposit

 

For CASD-NMR participants:

The required output data that all participants must deposit include:

  1. The automatically calculated structure, in PDB-compliant format. The number of conformers to be included in the bundle is left at your discernment. Please remember that we will input your structure to validation programs, therefore apply all refinement steps as if you were to submit the structure to the PDB.
     
  2. If relevant, the list(s) of all restraints generated and used in calculations, in particular dihedral angle restraints and distance restraints, 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). Note that these lists are needed also for validation purposes.
     
  3. A clear reference to the programs used and a short description of the protocol(s) adopted (e.g., for restrained molecular dynamics refinement)
     

What will we do with the data?

After the 8 weeks hold has elapsed, your output data will be sent to validation analysis, using the CING and PSVS packages, and will be compared to the reference structure. Note that at this point the reference structure may not be publicly available yet. In this case, unless the data depositor allows us to do so, we will not disclose your coordinates nor images depicting the structure itself. Z-scores and rmsd values to the reference structure will instead be made publicly available as soon as the analyses are completed. Your data as well as the entire validation results will be moved to the public part of the web site as soon as the reference structure is released by the PDB.
 

How to submit?

Please upload all the materials above to the CASD-NMR database (max. size for a single file: 2 Mb).
 
 
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Cite WeNMR

 
Usage of the WeNMR portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
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