News
Version 2 NMR Restraint Files Available from the wwPDB FTP
06/29
A new set of NMR restraint data files have been added to the wwPDB FTP with this update. These restraint files, identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current archive. Restraint files containing restraint data as originally deposited (Version 1 files) will remain on the site and will continue to be updated regularly as new NMR entries are released.
The Version 2 NMR restraint files were generated for the wwPDB by the BMRB in collaboration with PDBe and the Centre for Molecular and Biomolecular Informatics/Institute for Molecules and Materials at the Radboud University Nijmegen. NMR restraints were parsed from their original format (Version 1), and harmonized with the coordinates using the software packages Wattos (BMRB; and CMBI/IMM), FormatConverter and NMRStarExport (PDBe), and the CCPN framework. The complexity of this process may have led to minor modifications or loss of data in the Version 2 restraint files due to parsing or conversion errors. The PDB coordinate file and the Version 1 restraint files remain the primary reference for these data. More information about the process used to generate these files is available (1-3).
The initial release of the Version 2 NMR restraint files added more than 5700 new files (~310 Mbytes) to the FTP site. Version 2 restraint files for new PDB entries will be processed and made available after the PDB entry has been released. Version 1 restraint files for new PDB entries will continue to be released weekly.
NMR restraint files are named using extension .mr, as in "1abc.mr.gz" for PDB ID 1abc. Version 2 restraint files will be named "1abc_mr.str.gz", where "str" identifies the NMR-STAR (V3.1) data format. All restraint files are compressed (.gz) using the GNU gzip program.
Version 1 restraint files will remain in their current directory
structure. Version 2 restraint files are stored in directories named
by the middle two characters of the 4-character PDB ID in:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/nmr_restraints_v2/
These data files are linked symbolically to the single directory:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/nmr_restraints_v2/
- JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32: 1-12.
- WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL Markley, J Ionides, and ED Laue (2005). The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59: 687-696.
- JF Doreleijers, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45: 389-396. doi: 10.1007/s10858-009-9378-z
