Journal of Biomolecular NMR

, Volume 59, Issue 2, pp 75–86 | Cite as

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming

Article

Abstract

Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on ‘slices’, which are one-dimensional vectors in three-dimensional spectra that correspond to certain (\(N, H\)) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Keywords

Resonance assignment Peak picking Spin system  Wavelet 

Supplementary material

10858_2014_9828_MOESM1_ESM.pdf (251 kb)
Supplementary material 1 (f 252 KB)

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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Ahmed Abbas
    • 1
  • Xianrong Guo
    • 2
  • Bing-Yi Jing
    • 3
  • Xin Gao
    • 1
  1. 1.Computer, Electrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
  2. 2.Imaging and Characterization Core LabKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
  3. 3.Department of MathematicsHong Kong University of Science and TechnologyKowloonHong Kong

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