Deep neural network processing of DEER data

Science Advances
Steven G WorswickIlya Kuprov

Abstract

The established model-free methods for the processing of two-electron dipolar spectroscopy data [DEER (double electron-electron resonance), PELDOR (pulsed electron double resonance), DQ-EPR (double-quantum electron paramagnetic resonance), RIDME (relaxation-induced dipolar modulation enhancement), etc.] use regularized fitting. In this communication, we describe an attempt to process DEER data using artificial neural networks trained on large databases of simulated data. Accuracy and reliability of neural network outputs from real experimental data were found to be unexpectedly high. The networks are also able to reject exchange interactions and to return a measure of uncertainty in the resulting distance distributions. This paper describes the design of the training databases, discusses the training process, and rationalizes the observed performance. Neural networks produced in this work are incorporated as options into Spinach and DeerAnalysis packages.

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Citations

Jul 12, 2019·Journal of Biomolecular NMR·D Flemming Hansen
Sep 7, 2019·Angewandte Chemie·Xiaobo QuZhong Chen
Jun 2, 2020·Physical Chemistry Chemical Physics : PCCP·Svetlana KucherHeinz-Jürgen Steinhoff
Dec 5, 2019·Nature Communications·Timo StrohäkerMarkus Zweckstetter
Sep 25, 2020·Physical Chemistry Chemical Physics : PCCP·K KellerG Jeschke
Jan 2, 2020·Biophysical Journal·Diego Del AlamoJens Meiler
Jan 23, 2021·PLoS Computational Biology·Giulio TeseiKresten Lindorff-Larsen
Jan 28, 2021·Proceedings of the National Academy of Sciences of the United States of America·Jake L AmeyIlya Kuprov
Mar 3, 2021·Proceedings of the National Academy of Sciences of the United States of America·Pratibha KumariCédric Eichmann
Apr 9, 2021·The Journal of Physical Chemistry Letters·Svetlana KucherEnrica Bordignon
Apr 20, 2021·Journal of Biomolecular NMR·Gogulan Karunanithy, D Flemming Hansen
Apr 23, 2021·Scientific Reports·Sandra J FriesElke Deuerling
Apr 22, 2021·Physical Chemistry Chemical Physics : PCCP·Anna G MatveevaMichael K Bowman
Apr 30, 2021·Frontiers in Molecular Biosciences·Irina RitschGunnar Jeschke
Jun 17, 2021·PLoS Computational Biology·Diego Del AlamoHassane S Mchaourab
Feb 23, 2019·The Journal of Physical Chemistry Letters·Alexander T TaguchiRobert G Griffin
Jul 3, 2020·The Journal of Physical Chemistry. a·Sarah R SwegerStefan Stoll
Sep 17, 2021·The Journal of General Physiology·Eric J HustedtHassane S Mchaourab
Dec 14, 2021·Biophysical Journal·Burkhard EndewardXianyang Fang

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Methods Mentioned

BETA
electron paramagnetic resonance
electron resonance
two-electron dipolar spectroscopy

Software Mentioned

MATLAB
DEER
Spinach
DeerAnalysis
DEERNet

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