Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Structural and Functional Bioinformatics Group
Online Publication Date2015-01-26
Print Publication Date2015-07
Permanent link to this recordhttp://hdl.handle.net/10754/344037
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AbstractDenoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet's performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.
CitationMedian Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra 2015, 5:8017 Scientific Reports
SponsorsThis work was supported by the independent group leader starting grant of the Technische Universita¨t Dresden (TUD), and Award No. GRP-CF-2011-19-P-Gao-Huang and a GMSV-OCRF award from King Abdullah University of Science and Technology (KAUST).
PubMed Central IDPMC4306135
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