New Features

NMR data distribution in a unified format at the PDB


The wwPDB partners are pleased to announce that as of March 2020 the OneDep system will begin accepting upload of NMR experimental data as a single file, either in NMR-STAR or NEF format. This will start the transition from the current practice where distinct types of NMR data such as assigned chemical shifts, restraints, and peak lists are uploaded separately.

NMR-STAR is the official wwPDB format for storing NMR data, supported by an extensive dictionary [GitHub; Ulrich, E. L. et al. (2019) NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments Journal of Biomolecular NMR, 73: 5–9. doi: 10.1007/s10858-018-0220-3], while NEF (NMR exchange format; Gutmanas et al. (2015) NMR Exchange Format: a unified and open standard for representation of NMR restraint data Nature Structural & Molecular Biology 22: 433–434 doi: 10.1038/nsmb.3041) is a light-weight format and dictionary, supported by the leading software in NMR structure determination. The use of these two interconvertible standard formats as single data files will simplify the process of deposition, as well as the storage and distribution of this data.

For newly deposited entries accompanied by such a unified data file, the NMR data will be distributed in the PDB FTP area as single files in the NMR-STAR format. A best effort conversion to the NEF format will also be provided. These unified NMR data files will be added to a new FTP directory, “nmr_data” in parallel to the existing directories, nmr_restraints and nmr_chemical shifts. In addition, to support existing users these unified files that contain both restraints and chemical shift data will be copied to the existing directories “nmr_restraints” and “nmr_chemical_shifts”.

A standardized naming convention for NMR unified data will also be developed to simplify access of the relevant NMR data. File naming will start with PDB accession code, followed by nmr_data with format type extension, for example ‘2lcb_nmr_data.nef’ or ‘2lcb_nmr_data.str’.

We plan to begin accepting and distributing NMR data as unified files from March 2020.