Journal of Biomolecular NMR

, Volume 47, Issue 2, pp 85–99 | Cite as

A probabilistic approach for validating protein NMR chemical shift assignments

Article

Abstract

It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3–6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called “Probabilistic Approach for protein Nmr Assignment Validation (PANAV)” and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

Keywords

NMR Protein chemical shift Chemical shift assignment Chemical shift assignment validation BioMagResBank (BMRB) 

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Shanghai American School PudongSan Jia Gang, Pudong, ShanghaiPeople’s Republic of China
  2. 2.Little RockUSA
  3. 3.Departments of Computing Science and Biological SciencesUniversity of AlbertaEdmontonCanada

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