ArticleThe journal of physical chemistry. A2019
Singular Value Decomposition Method To Determine Distance Distributions in Pulsed Dipolar Electron Spin Resonance: II. Estimating Uncertainty.
Article in The journal of physical chemistry. A, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Localized Reconstruction of Multimodal Distance Distribution from DEER Data of Biopolymers.bioRxiv : the preprint server for biology · 2025Article
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- MRI Denoising Using Pixel-Wise Threshold Selection.IEEE access : practical innovations, open solutions · 2024Article
- Insights into the oligomeric structure of the HIV-1 Vpu protein.Journal of structural biology · 2023Article
- Membrane Binding Induces Distinct Structural Signatures in the Mouse Complexin-1C-Terminal Domain.Journal of molecular biology · 2023Article
- Protein delivery to living cells by thermal stimulation for biophysical investigation.Scientific reports · 2022Article
- Mechanistic insight into light-dependent recognition of Timeless by Drosophila Cryptochrome.Structure (London, England : 1993) · 2022Article
- Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules.Journal of the American Chemical Society · 2021Article
- Protein functional dynamics from the rigorous global analysis of DEER data: Conditions, components, and conformations.The Journal of general physiology · 2021Article
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- Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER distance restraints.PLoS computational biology · 2021Article
- Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels.European biophysics journal : EBJ · 2021Review
- Engineered chemotaxis core signaling units indicate a constrained kinase-off state.Science signaling · 2020Article
- Probing the Interaction between HIV-1 Protease and the Homodimeric p66/p66' Reverse Transcriptase Precursor by Double Electron-Electron Resonance EPR Spectroscopy.Chembiochem : a European journal of chemical biology · 2020Article
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- Submillisecond Freezing Permits Cryoprotectant-Free EPR Double Electron-Electron Resonance Spectroscopy.Chemphyschem : a European journal of chemical physics and physical chemistry · 2020Article
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2 authors.
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Abstract
This paper is a continuation of the method introduced by Srivastava and Freed (2017) that is a new method based on truncated singular value decomposition (TSVD) for obtaining physical results from experimental signals without any need for Tikhonov regularization or other similar methods that require a regularization parameter. We show here how to estimate the uncertainty in the SVD-generated solutions. The uncertainty in the solution may be obtained by finding the minimum and maximum values over which the solution remains converged. These are obtained from the optimum range of singular value contributions, where the width of this region depends on the solution point location (e.g., distance) and the signal-to-noise ratio (SNR) of the signal. The uncertainty levels typically found are very small with substantial SNR of the (denoised) signal, emphasizing the reliability of the method. With poorer SNR, the method is still satisfactory but with greater uncertainty, as expected. Pulsed dipolar electron spin resonance spectroscopy experiments are used as an example, but this TSVD approach is general and thus applicable to any similar experimental method wherein singular matrix inversion is needed to obtain the physically relevant result. We show that the Srivastava-Freed TSVD method along with the estimate of uncertainty can be effectively applied to pulsed dipolar electron spin resonance signals with SNR > 30, and even for a weak signal (e.g., SNR ≈ 3) reliable results are obtained by this method, provided the signal is first denoised using wavelet transforms (WavPDS).
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