Publication date: Available online 1 February 2018 Source:Journal of Magnetic Resonance
Author(s): Thomas H. Edwards, Stefan Stoll
Tikhonov regularization is the most commonly used method for extracting distance distributions from experimental double electron-electron resonance (DEER) spectroscopy data. This method requires the selection of a regularization parameter, ? , and a regularization operator, L. We analyze the performance of a large set of ? selection methods and several regularization operators, using a test set of over half a million synthetic noisy DEER traces. These are generated from distance distributions obtained from in silico double labeling of a protein crystal structure of T4 lysozyme with the spin label MTSSL. We compare the methods and operators based on their ability to recover the model distance distributions from the noisy time traces. The results indicate that several ? selection methods perform quite well, among them the Akaike information criterion and the generalized cross validation with either the first- or second-derivative operator. They perform significantly better than currently utilized L-curve methods. Graphical abstract
[NMR paper] A Bayesian approach to quantifying uncertainty from experimental noise in DEER spectroscopy
A Bayesian approach to quantifying uncertainty from experimental noise in DEER spectroscopy
Publication date: Available online 2 July 2016
Source:Journal of Magnetic Resonance</br>
Author(s): Thomas H. Edwards, Stefan Stoll</br>
Double Electron-Electron Resonance (DEER) spectroscopy is a solid-state pulse Electron Paramagnetic Resonance (EPR) experiment that measures distances between unpaired electrons, most commonly between protein-bound spin labels separated by 1.5-8 nm. From the experimental data, a distance distribution P ( r ) is extracted using...
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[NMR paper] The determination of pair distance distribution by double electron-electron resonance: Regularization by the length of distance discretization with Monte Carlo calculations
The determination of pair distance distribution by double electron-electron resonance: Regularization by the length of distance discretization with Monte Carlo calculations
Publication date: Available online 2 June 2016
Source:Journal of Magnetic Resonance</br>
Author(s): Sergei A. Dzuba</br>
Pulsed double electron-electron resonance technique (DEER, or PELDOR) is applied to study conformations and aggregation of peptides, proteins, nucleic acids, and other macromolecules. For a pair of spin labels, experimental data allows for determination of their distance...
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[NMR paper] Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms.
Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms.
Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms.
J Biomol NMR. 2015 Mar 26;
Authors: Sun S, Gill M, Li Y, Huang M, Byrd RA
Abstract
The advantages of non-uniform sampling (NUS) in offering time savings and resolution enhancement in NMR experiments have been increasingly recognized. The possibility of sensitivity...
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03-27-2015 11:59 PM
Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms
Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms
Abstract
The advantages of non-uniform sampling (NUS) in offering time savings and resolution enhancement in NMR experiments have been increasingly recognized. The possibility of sensitivity gain by NUS has also been demonstrated. Application of NUS to multidimensional NMR experiments requires the selection of a sampling scheme and a reconstruction scheme to generate uniformly sampled time domain data. In this report, an...
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03-25-2015 10:58 PM
[NMR paper] Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination.
Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Applications of NMR-based PRE and EPR-based DEER spectroscopy to homodimer chain exchange characterization and structure determination.
Methods Mol Biol. 2014;1091:215-27
Authors: Yang Y, Ramelot TA, Ni S, McCarrick RM, Kennedy MA
Abstract
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[NMR paper] The Fantastic Four: A plug 'n' play set of optimal control pulses for enhancing NMR spectroscopy.
From Mendeley Biomolecular NMR group:
The Fantastic Four: A plug 'n' play set of optimal control pulses for enhancing NMR spectroscopy.
Journal of magnetic resonance (San Diego, Calif. : 1997) (2013). Pages: 16-31. Manoj Nimbalkar, Burkhard Luy, Thomas E Skinner, Jorge L Neves, Naum I Gershenzon, Kyryl Kobzar, Wolfgang Bermel, Steffen J Glaser et al.
We present highly robust, optimal control-based shaped pulses designed to replace all 90° and 180° hard pulses in a given pulse sequence for improved performance. Special attention was devoted to ensuring that the pulses can be simply...
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10-17-2013 12:49 PM
[NMR paper] The Fantastic Four: A plug 'n' play set of optimal control pulses for enhancing NMR spectroscopy.
From Mendeley Biomolecular NMR group:
The Fantastic Four: A plug 'n' play set of optimal control pulses for enhancing NMR spectroscopy.
Journal of magnetic resonance (San Diego, Calif. : 1997) (2013). Pages: 16-31. Manoj Nimbalkar, Burkhard Luy, Thomas E Skinner, Jorge L Neves, Naum I Gershenzon, Kyryl Kobzar, Wolfgang Bermel, Steffen J Glaser et al.
We present highly robust, optimal control-based shaped pulses designed to replace all 90° and 180° hard pulses in a given pulse sequence for improved performance. Special attention was devoted to ensuring that the pulses can be simply...
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04-11-2013 03:08 PM
DEER-Stitch: Combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data
DEER-Stitch: Combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
J.E. Lovett, B.W. Lovett, J. Harmer</br>
Over approximately the last fifteen years the electron paramagnetic resonance (EPR) technique of double electron electron resonance (DEER) has attracted considerable attention since it allows for the precise measurement of the dipole-dipole coupling between radicals and thus can lead to distance information between pairs of radicals separated by up to ca. 8 nm....
Optimal Tikhonov Regularization for DEER Spectroscopy
Linear Mode
