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Bioinformatics Vol. 19 no. 16 2003
pages 2054-2064
© 2003 Oxford University Press

Protein structural class identification directly from NMR spectra using averaged chemical shifts*

S.P. Mielke 1,2 and V.V. Krishnan 2,{dagger}

1 Biophysics Graduate Group, University of California, Davis, CA 95616, USA and 2 Molecular Biophysics Group, L-448 Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA

Received on January 6, 2003 ; revised on March 19, 2003 ; accepted on March 28, 2003

Knowledge of the three-dimensional structure of proteins is integral to understanding their functions, and a necessity in the era of proteomics. A wide range of computational methods is employed to estimate the secondary, tertiary, and quaternary structures of proteins. Comprehensive experimental methods, on the other hand, are limited to nuclear magnetic resonance (NMR) and X-ray crystallography. The full characterization of individual structures, using either of these techniques, is extremely time intensive. The demands of high throughput proteomics necessitate the development of new, faster experimental methods for providing structural information. As a first step toward such a method, we explore the possibility of determining the structural classes of proteins directly from their NMR spectra, prior to resonance assignment, using averaged chemical shifts. This is achieved by correlating NMR-based information with empirical structure-based information available in widely used electronic databases. The results are analyzed statistically for their significance. The robustness of the method as a structure predictor is probed by applying it to a set of proteins of unknown structure. Our results show that this NMR-based method can be used as a low-resolution tool for protein structural class identification.

* The authors dedicate this manuscript with affection and admiration to Prof. Robert E. Feeney, Department of Food Sciences and Technology, University of California, Davis, on his 90th birthday.

{dagger} To whom correspondence should be addressed.


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