RefDB: Re-referenced Protein Chemical Shift Database

RefDB website

In case of the BMRB, it is known that a significant portion of depositions use different or non-IUPAC chemical shift reference standards. This lack of uniformity makes it difficult to extract sequence/structure relationships from chemical shifts. Nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. In addition, it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC (13)C and (15)N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced.

The RefDB is a database consisting of more than 2100 proteins -- all of which have been computationally re-referenced to DSS. RefDB is a continuously updated resource that uses web-bots to query public databases (BMRB, GenBank, PDB) and fetch assignment, sequence and structure data on a weekly basis. It then applies a series of data checking routines (using keywords to remove paramagnetic or denatured proteins) followed by a series of calculations to identify and correct chemical shift referencing errors. RefDB is fully web-enabled, it stores its data in two standard formats (NMR-Star and Shifty), it performs automated data updating, checking and validation and it provides open access to its data in a fully downloadable flat file format as well as in a hyperlinked browsable table (see attached Figure). RefDB also supports keyword queries and sequence searches (using local BLAST). RefDB is updated weekly and the database, along with its associated software, is freely available at http://refdb.wishartlab.com and the BMRB website.

Related Program:
- SHIFTX
- SHIFTCOR

Developed by Dr. Wishart's Lab

Attached Images

Refdb-table.jpg (20.3 KB, 1 views)

Last edited by gwnmr; 01-10-2012 at 06:37 PM.

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