Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Aug;38(4):289-302.
doi: 10.1007/s10858-007-9166-6. Epub 2007 Jul 4.

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

Yang Shen  1 , Ad Bax
Affiliations

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

Yang Shen et al. J Biomol NMR. 2007 Aug.

Abstract

Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in phi/psi/chi(1 )torsion angles and sequence similarity to the query triplet of interest. The database contains (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C' chemical shifts for 200 proteins for which a high resolution X-ray (< or =2.4 A) structure is available. The relative importance of the weighting factors for the phi/psi/chi(1) angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for (15)N, (1)H(N), (1)H(alpha), (13)C(alpha), (13)C(beta) and (13)C', respectively, including outliers.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. J Am Chem Soc. 2002 Nov 27;124(47):14075-84 - PubMed
    1. Biochemistry. 1990 Aug 7;29(31):7201-14 - PubMed
    1. J Biomol NMR. 1997 Sep;10(2):129-42 - PubMed
    1. J Biomol NMR. 1999 Mar;13(3):289-302 - PubMed
    1. J Mol Biol. 1995 Apr 7;247(4):541-6 - PubMed

Publication types

LinkOut - more resources