NMR Restraints Grid

Howto

• Getting started
• Download data
• Faq
• Use downloaded data
• Link to NMR Restraints Grid
• Link to images of PDB entries
• Known bugs and todo list
• NMR data format descriptions
• References
• Funding

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.

• Get all data in the DOCR database (ref 1).
  
  1. Start by selecting the NMR Restraints Grid so that the default options are used.
  2. Select 3-converted-DOCR for Stage
  3. Select Blocks for Show
  4. Leave the other options to their default values and do submit
  5. The resulting page shows a table of block counts for different data types for/from many different programs. Select all blocks by selecting the link in the cell for which both column and row are labeled total. It will take a while to download and render on your computer because there are many blocks to show.
  6. The resulting page shows another table with the PDB entry codes (in the column labeled pdb_id) of entries in DOCR. 
  7. To save the actual data, select the icon labeled: Save to zip file containing files for each block. This will start to download a zipped file that contains a separate file for each block in the selection made up to this point. The blocks are named only by their block identifier (a unique number for each block in the database) and change over time so please don't use them for future reference. A README and index file will also be included in the download.
  8. WARNING: This is a lot of data so be ready to wait or cancel the streaming at this point.
• Get all PDB entry codes containing a certain type (e.g. RDCs) of data and then get the original (raw/deposited) data.
  1. Start by selecting the NMR Restraints Grid so that the default options are used.
  2. Select 1-converted for Stage.
  3. Do a submit.
  4. The resulting page shows a list of files containing many different data types for/from many different programs. Select the link for the total number of files (in the column labeled Total) with among other data types the data type you're interested in, like dipolar coupling for RDCs.
  5. The resulting page shows another table with the PDB entry codes (in the column labeled pdb_id) of entries that have RDCs as part of the deposited data. 
  6. To save the actual data, select the icon labeled: Save to zip file containing files for each block. This will start to download a zipped file that contains a separate file for each block in the selection made up to this point. The blocks are named only by their block identifier (a unique number for each block in the database) and change over time so please don't use them for future reference. A README and index file will also be included in the download.
• Get all STAR formatted data with one file for each PDB entry.
  1. Start by selecting the NMR Restraints Grid so that the default options are used.
  2. Select 2-parsed for Stage.
  3. Select show Blocks.
  4. Do a submit.
  5. From the resulting page select the link for the number of blocks where the values to Type and Subtype are all entry and full and is in the column under STAR.
     Note that the information on program and data type is no longer preserved at the block level because everything is in one text block, e.g. NOEs and RDCs will be merged into one block.
  6. To save the actual data, select the icon labeled: Save to zip file containing files for each block. This will start to download a zipped file that contains a separate file for each block in the selection made up to this point. The blocks are named only by their block identifier (a unique number for each block in the database) and change over time so please don't use them for future reference. A README and index file will also be included in the download.

Faq

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

• Top level
• Individual entry (E.g. BMRB id 4010)
• Individual entry (E.g. PDB id 1XMW)

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

• Individual entry (E.g. PDB code 1XMW)
• Indexed by BMRB id
• Indexed by PDB id NEW

Known bugs and todo list

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.

References

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:

• Bijvoet Center for Biomolecular Research, (Utrecht University, the Netherlands),
• BMRB (Madison, WI, USA),
• Proteins Biophysics, IMM, (Radboud University Nijmegen, the Netherlands),
• CCPN, and
• PDBe, Protein Data Bank Europe, (Hinxton, United Kingdom). 

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

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'