Literature DB >> 30685560

General regularization framework for DEER spectroscopy.

Luis Fábregas Ibáñez1, Gunnar Jeschke2.   

Abstract

Tikhonov regularization is the standard processing technique for the inversion of double electron-electron resonance (DEER) data to distance distributions without assuming a parametrized model. In other fields it has been surpassed by modern regularization methods. We analyze such alternative regularization methods based on the Tikhonov, total variation (TV) and Huber penalties with and without the use of Bregman iterations. For this, we provide a general mathematical framework and its open-source software implementation. We extend an earlier approach by Edwards and Stoll for the selection of an optimal regularization parameter to all of these penalties and use their big test data set of noisy DEER traces with known ground truth for assessment. The results indicate that regularization methods based on Bregman iterations provide an improvement upon Tikhonov regularization in recognizing features and recovering distribution width at moderate signal-to-noise ratio, provided that noise variance is known. Bregman-iterative methods are robust with respect to the method used in the choice of regularization parameter.
Copyright © 2019 Elsevier Inc. All rights reserved.

Keywords:  Bregman iterations; DEER; Distance distributions; EPR; Huber; Inverse problem; Optimization; PELDOR; Regularization; Tikhonov; Total variation

Year:  2019        PMID: 30685560     DOI: 10.1016/j.jmr.2019.01.008

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  3 in total

Review 1.  Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels.

Authors:  Igor Tkach; Ulf Diederichsen; Marina Bennati
Journal:  Eur Biophys J       Date:  2021-02-28       Impact factor: 1.733

2.  Protein functional dynamics from the rigorous global analysis of DEER data: Conditions, components, and conformations.

Authors:  Eric J Hustedt; Richard A Stein; Hassane S Mchaourab
Journal:  J Gen Physiol       Date:  2021-09-16       Impact factor: 4.086

3.  A Two-Armed Probe for In-Cell DEER Measurements on Proteins*.

Authors:  Qing Miao; Enrico Zurlo; Donny de Bruin; Joeri A J Wondergem; Monika Timmer; Anneloes Blok; Doris Heinrich; Mark Overhand; Martina Huber; Marcellus Ubbink
Journal:  Chemistry       Date:  2020-11-17       Impact factor: 5.236

  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.