BMRB Query Grid Interface Description


Introduction

The query grid interface provides a mechanism for retrieving sets of entries that fit the criteria of predefined queries from the BMRB archive. The query criteria are described by the headings for the rows and columns in each grid. For example, from the main grid, if one clicks on the link in the box in the grid that is at the intersection of the column labeled 'DNA' and the row labeled '1H Chemical Shifts,' they will be taken to a page containing a listing of all of the BMRB entries that have 1H chemical shifts for DNA polymers. If one selects the grid box 'Proteins/Peptides,' a page containing a link to an HTML page listing all of the entries as well as a new query grid that can be used to further refine the query. In many cases, the result of a query can be displayed with the entries sorted by the number of 1H, 13C, 15N chemical shifts or BMRB accession number or PDB code. By selecting the 'Compressed file' link, it is possible to download a single compressed file that contains all of the entries returned by the current query.

Cautionary notes

The results obtained for any query will depend on the quality of the annotation for each entry. If ligands are not reported for a protein entry but do exist, the entry will still be included in the 'Protein only' query result. In general, entries with accession numbers below 4000 may appear in inappropriate query results for these reasons.

In some cases, it is important to think about how a query may have been constructed. If one selects 'DNA' from the main query grid, all of the entries where DNA was reported in the molecular system studied will be returned whether or not there is any quantitative data for the DNA. However, by selecting the link in the grid box corresponding to 'DNA' and 'All Chemical Shifts,' the entries containing DNA and where chemical shifts for the DNA were reported will be returned.

There are currently a few BMRB entries (~25) that are in an older format and are not included in the current queries.


  Back to the initial grid