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PDBe NMR home page

The NMR work at the PDBe comprises:

Collaboration with the CCPN project

The PDBe group has been collaborating with the Collaborative Computing Project for the NMR community (CCPN) since its inception in 2000. This involved both helping to define the CCPN data model, which forms the core of the CCPN framework, and testing this framework in practical situations.
 
We are also responsible for:

  • NMR toolkit (FormatConverter software): this is a widely used toolkit for import and export of many existing NMR data formats. This software is available for download together with the latest CCP data model here. It can also be downloaded from the CCPN website.
  • ChemComp data: the reference data for chemical compounds (ChemComps) used in the CCPN framework is derived from the E-MSD database. This information is combined with reference information generated separately (e.g. to identify prochiral centres), and reference information from the public domain (e.g. naming system information from the BioMagResBank). The final information is made available per chemical compound as XML files. This information is also reorganised and available as tabulated or XML files from the 'Reference data' pages.
  • NMR Experiment Prototype information: as part of the CCPN data model, the PDBe and CCPN developed a consistent and well-described generic standard for naming NMR experiments. The PDBe provides a list of the current set of included experiments on this website.
  • Deposition: It is now possible to upload a CCPN project file for deposition at the wwPDB and/or the BMRB.

Large scale NMR data analysis

Once NMR data is stored in the CCPN framework, it is highly organised and becomes much easier to analyse. We are analysing archived NMR data from the wwPDB and BMRB, and hope to show the NMR community that their deposited data is very useful, and that large scale analysis can provide very valuable information that can help in the day-to-day analysis and interpretation of NMR data.
 
The current efforts include:

  • Constraint data: An analysis of the constraint data of 1834 PDB entries shows that the information from the constraints provides an NMR-specific alternative for the information from the coordinates.
  • Chemical shift data: as part of a collaboration, we are in the process of analysing thousands of BMRB entries in relation to their coordinates, and will make the results from this analysis available later this year.
  • Implementations: A set of software using the results from the constraints data analysis will be available as part of the CCPN framework in the 2.0 release.
  • Olderado: all relevant NMR entries in the PDB are analysed with the NMRCore/NMRClust software to provide clustering information for NMR structure ensembles.

NMR data storage

  • The Databank for Experimental NMR data (DEN): this resource is being set up as a resource for software development. Raw NMR data is stored here, and all available information about the spectra is organized within the CCP data model, so that automatic procedures can be run easily on many sets of data.
  • Database of NMR data: an ongoing project consists of creating an NMR extension to the E-MSD database. In this NMR database information about the constraints lists used to generate the structures will be stored, as well as information on chemical shifts and other NMR parameters.
  • RECOORD data: we also provide the data from the RECOORD project.

Other

  • NMR data links at the PDBe: providing links to NMR data from the wwPDB entry pages.
  • COmplementary COordinates (COCO): a new method that provides information about the complexity and coverage of a given NMR structure ensemble. It also generates new conformers within the ensemble.

References


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