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NMR Restraints Grid

Data flows from the original raw data to parsed, to the databases DOCR and FRED


Getting started

  1. Start by selecting the NMR Restraints Grid so that the default options are used.
  2. Specify a PDB entry to find data for by entering its four-character code (E.g. 1A24)
  3. Select 0 for  Hide the grouped block counts for the software formats if there are less blocks than
  4. Do a submit by clicking on the Submit button
  5. Select the number by clicking on it, in the cell for which both row and column are labeled Total
  6. Select one of the blocks by clicking on the number in the cell where the column is labeled mrblock_id. E.g. select the block id for where the stage column reads: 3-converted-DOCR and the columns program, type, subtype and format read:  XPLOR/CNS, distance, NOE, ambi.
  7. Congratulations, the NOE distance restraints of entry 1A24 from the DOCR database will be on your screen
  8. Download a dataset by clicking on the icon at the top of the table. A README and index file will also be included in the download.
  9. More background info is available in the rest of this document.

Download data

Below are three other common usage patterns.


Find the number of restraints per residue

Use downloaded data

Unzip the downloaded compressed restraint data into a target directory of choice on your computer. The uncompressed files will a README that explains how to use the downloaded data.

Link to the NMR Restraints Grid

WARNING: The numeric identifiers for mrblock and mrfile in the database cannot be used as a reference, because they do change every so often. No garantee is made that the parameters (other than bmrb_id and pdb_id) will be maintained in the future, so if you must use them then please check back every so often.

A database dump in text format is made available every Thursday around 23h00 CDT. The file entry.txt in that location can be used to find all the entries in the NMR Restraints Grid.

The links between BMRB and PDB entries are based on the file score_many2one.csv available. It is updated every Thursday around 16h00 CDT. For more information on how the links were created and for lists of many more links look at the documentation directory at the same URL.

Link to the images of PDB entries


Known bugs and todo list

Please check the issues list at Google Code here.

NMR data format descriptions

The formats and how they are converted are described in Wattos Java documentation for Amber, Discover, Dyana, Emboss, and Xplor.

Actually, the JavaCC grammar descriptions (source code) give the most detailed description. The grammar files can be downloaded from Wattos home page.


The initial development of the NMR Restraints Grid was carried out at BMRB (ref 1). The converted and filtered databases DOCR and FRED (ref 2) were constructed as a collaborative project involving individuals from the:

The RECOORD database of REcalculated COORdinates (ref 3) was constructed using the FRED database. The DRESS database (ref 4) was constructed using the original restraints from the NMR Restraint Grid.

The software packages FormatConverter and Wattos were used to construct the DOCR and FRED databases.

Please cite these references when using the data:

  1. Doreleijers, J.F., Mading, S., Maziuk, D., Sojourner, K., Yin, L., Zhu, J., Markley, J.L., and Ulrich, E.L., J. Biomol. NMR 26, 139-146 (2003). medline
  2. Doreleijers J.F., Nederveen A.J., Vranken W., Lin J., Bonvin A.M., Kaptein R., Markley J.L., and Ulrich E.L. BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12 (2005). medline 
  3. Nederveen,A.J., Doreleijers,J.F., Vranken,W., Miller,Z., Spronk,C.A., Nabuurs,S.B., Guntert,P., Livny,M., Markley,J.L., Nilges,M., Ulrich,E.L., Kaptein,R. and Bonvin,A.M. (2005). RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59, 662-672. medline
  4. Nabuurs,S.B., Nederveen,A.J., Vranken,W., Doreleijers,J.F., Bonvin,A.M., Vuister,G.W., Vriend,G. and Spronk,C.A. (2004). DRESS: a database of REfined solution NMR structures. Proteins 55, 483-486. medline


Funding for the development of the DOCR and FRED databases came from:

BMRB: grant LM05799 from the National Library of Medicine, NIH
Proteins Biophysics, IMM/CMBI, Radboud University Nijmegen, the Netherlands
CCPN: Collaborative Computing Project for NMR
NMRQUAL: European Community Contract No. QLG2-CT-2000-01313 and
EU FP6 'ExtendNMR'

This file was last updated on: Thu Jan 15 10:29:07 CET 2009