DEER data analysis software: a comparative guide

Hannah Russell; Robyn Cura; Janet E. Lovett

doi:10.3389/fmolb.2022.915167

DEER data analysis software: a comparative guide

Hannah Russell, Robyn Cura, Janet E. Lovett^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

Pulsed Dipolar Spectroscopy (PDS) Electron Paramagnetic Resonance (EPR) experiments are popular techniques to measure dipolar coupling and therefore nanometre-scale distances and distance distributions between paramagnetic centres. The most common experiment is Double Electron Electron Resonance (DEER, also known as PELDOR), which is a well-tested and documented experiment. Until recently there were few methods to analyze data, however this has changed of late. The current plethora of DEER analysis packages may appear overwhelming to a new practitioner of DEER. In this work, six of the most popular packages are reviewed. This includes a brief guide for getting started with the environments, and qualitative testing and comparison of each using both simulated and experimental DEER data.

Original language	English
Article number	915167
Number of pages	17
Journal	Frontiers in Molecular Biosciences
Volume	9
DOIs	https://doi.org/10.3389/fmolb.2022.915167
Publication status	Published - 1 Jun 2022

Keywords

EPR/ESR
DEER/PELDOR
Pulsed dipolar spectroscopy
DeerAnalysis
DEERnet
Tikhonov regularization
Neural networks
Gaussian models

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10.3389/fmolb.2022.915167Licence: CC BY

Russell-2022-DEER-data-analysis-software-FMOLB-09-915167-CCBY
Copyright © 2022 Russell, Cura and Lovett. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Final published version, 3.53 MBLicence: CC BY

Cite this

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title = "DEER data analysis software: a comparative guide",

abstract = "Pulsed Dipolar Spectroscopy (PDS) Electron Paramagnetic Resonance (EPR) experiments are popular techniques to measure dipolar coupling and therefore nanometre-scale distances and distance distributions between paramagnetic centres. The most common experiment is Double Electron Electron Resonance (DEER, also known as PELDOR), which is a well-tested and documented experiment. Until recently there were few methods to analyze data, however this has changed of late. The current plethora of DEER analysis packages may appear overwhelming to a new practitioner of DEER. In this work, six of the most popular packages are reviewed. This includes a brief guide for getting started with the environments, and qualitative testing and comparison of each using both simulated and experimental DEER data. ",

keywords = "EPR/ESR, DEER/PELDOR, Pulsed dipolar spectroscopy, DeerAnalysis, DEERnet, Tikhonov regularization, Neural networks, Gaussian models",

author = "Hannah Russell and Robyn Cura and Lovett, {Janet E.}",

note = "We acknowledge financial support from EPSRC (studentship to HR EP/R513337/1 and The Royal Society (URF to JEL UR150698F). The UKRI block grant to St Andrews supported the journal charges for open access.",

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language = "English",

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T2 - a comparative guide

AU - Russell, Hannah

AU - Cura, Robyn

AU - Lovett, Janet E.

N1 - We acknowledge financial support from EPSRC (studentship to HR EP/R513337/1 and The Royal Society (URF to JEL UR150698F). The UKRI block grant to St Andrews supported the journal charges for open access.

PY - 2022/6/1

Y1 - 2022/6/1

N2 - Pulsed Dipolar Spectroscopy (PDS) Electron Paramagnetic Resonance (EPR) experiments are popular techniques to measure dipolar coupling and therefore nanometre-scale distances and distance distributions between paramagnetic centres. The most common experiment is Double Electron Electron Resonance (DEER, also known as PELDOR), which is a well-tested and documented experiment. Until recently there were few methods to analyze data, however this has changed of late. The current plethora of DEER analysis packages may appear overwhelming to a new practitioner of DEER. In this work, six of the most popular packages are reviewed. This includes a brief guide for getting started with the environments, and qualitative testing and comparison of each using both simulated and experimental DEER data.

AB - Pulsed Dipolar Spectroscopy (PDS) Electron Paramagnetic Resonance (EPR) experiments are popular techniques to measure dipolar coupling and therefore nanometre-scale distances and distance distributions between paramagnetic centres. The most common experiment is Double Electron Electron Resonance (DEER, also known as PELDOR), which is a well-tested and documented experiment. Until recently there were few methods to analyze data, however this has changed of late. The current plethora of DEER analysis packages may appear overwhelming to a new practitioner of DEER. In this work, six of the most popular packages are reviewed. This includes a brief guide for getting started with the environments, and qualitative testing and comparison of each using both simulated and experimental DEER data.

KW - EPR/ESR

KW - DEER/PELDOR

KW - Pulsed dipolar spectroscopy

KW - DeerAnalysis

KW - DEERnet

KW - Tikhonov regularization

KW - Neural networks

KW - Gaussian models

UR - https://www.frontiersin.org/articles/10.3389/fmolb.2022.915167/abstract

U2 - 10.3389/fmolb.2022.915167

DO - 10.3389/fmolb.2022.915167

M3 - Article

SN - 2296-889X

VL - 9

JO - Frontiers in Molecular Biosciences

JF - Frontiers in Molecular Biosciences

M1 - 915167

ER -

DEER data analysis software: a comparative guide

Abstract

Keywords

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RS Research Fellowship Renewal: Biological Structure Determination by EPR Spectroscopy: The Next Steps

Under Pressure: Measuring Nanometre Distance Changes in Biomolecules (thesis data)