Related ArticlesMedian Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra.
Sci Rep. 2015;5:8017
Authors: Cannistraci CV, Abbas A, Gao X
Abstract
Denoising 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.
PMID: 25619991 [PubMed - as supplied by publisher]
[NMR paper] Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.
Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.
J Biomol NMR. 2014 Jun;59(2):57-73
Authors: Suiter CL, Paramasivam S, Hou G, Sun S, Rice D, Hoch JC, Rovnyak D, Polenova T
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12-31-2014 06:44 PM
Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range
Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range
Abstract
Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high...
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06-19-2014 10:21 PM
[NMR paper] Nonlinear excitations match correlated motions unveiled by NMR in proteins: a new perspective on allosteric cross-talk.
Nonlinear excitations match correlated motions unveiled by NMR in proteins: a new perspective on allosteric cross-talk.
Nonlinear excitations match correlated motions unveiled by NMR in proteins: a new perspective on allosteric cross-talk.
Phys Biol. 2014 Apr 15;11(3):036003
Authors: Piazza F
Abstract
In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated...
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04-16-2014 11:07 AM
[NMR paper] A molecular dynamics simulations-based interpretation of NMR multidimensional heteronuclear spectra of alpha-synuclein/dopamine adducts.
A molecular dynamics simulations-based interpretation of NMR multidimensional heteronuclear spectra of alpha-synuclein/dopamine adducts.
Related Articles A molecular dynamics simulations-based interpretation of NMR multidimensional heteronuclear spectra of alpha-synuclein/dopamine adducts.
Biochemistry. 2013 Aug 21;
Authors: Dibenedetto D, Rossetti G, Caliandro R, Carloni P
Abstract
Multidimensional heteronuclear NMR spectroscopy provides valuable structural information on adducts between naturally unfolded proteins and their ligands....
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08-24-2013 04:53 PM
[NMRpipe Yahoo group] Re: Denoising the spectra using SVD approach
Re: Denoising the spectra using SVD approach
Dear Frank, Is there any module available to denoise 1D spectrum using SVD approach? Kindly let me know, i would like to use it for my 1D complex data. Thanks!
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12-20-2011 04:09 AM
[Question from NMRWiki Q&A forum] c13 filter noesy experment for homodimer protein
c13 filter noesy experment for homodimer protein
Dear wikiers
I would like to take c13 filter noesy experment for homodimer protein , total 20 kd size . could you please suggest which parameters should i consider more specificly while taking this experment to get best signal because i dont want to try on trial and error method. any knid of help is greatly appreciated
Thanking you in advance
Regards sri
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06-30-2011 05:06 PM
[NMR paper] A modified strategy for sequence specific assignment of protein NMR spectra based on
A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments.
Related Articles A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments.
J Biomol NMR. 2005 Feb;31(2):115-28
Authors: Schubert M, Labudde D, Leitner D, Oschkinat H, Schmieder P
The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step....
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11-24-2010 11:14 PM
[NMR paper] Prospects for resonance assignments in multidimensional solid-state NMR spectra of un
Prospects for resonance assignments in multidimensional solid-state NMR spectra of uniformly labeled proteins.
Related Articles Prospects for resonance assignments in multidimensional solid-state NMR spectra of uniformly labeled proteins.
J Biomol NMR. 1996 Oct;8(3):239-51
Authors: Tycko R
The feasibility of assigning the backbone 15N and 13C NMR chemical shifts in multidimensional magic angle spinning NMR spectra of uniformly isotopically labeled proteins and peptides in unoriented solid samples is assessed by means of numerical simulations....
Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra.
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