Methyl-TROSY nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterising large biomolecules in solution. However, preparing samples for these experiments is demanding and entails deuteration, limiting its use. Here we demonstrate that NMR spectra recorded on protonated, uniformly ^(13)C labelled samples can be processed using deep neural networks to yield spectra that are of similar quality to typical deuterated methyl-TROSY spectra, potentially providing information...
Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks
Towards autonomous analysis of chemical exchange saturation transfer experiments using deep neural networks
Abstract
Macromolecules often exchange between functional states on timescales that can be accessed with NMR spectroscopy and many NMR tools have been developed to characterise the kinetics and thermodynamics of the exchange processes, as well as the structure of the conformers that are involved. However, analysis of the NMR data that report on exchanging macromolecules often hinges on complex least-squares fitting procedures as well as human...
nmrlearner
Journal club
0
05-29-2022 03:31 AM
[NMR paper] DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra
DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra
The analysis of nuclear magnetic resonance (NMR) spectra for the comprehensive and unambiguous identification and characterization of peaks is a difficult, but critically important step in all NMR analyses of complex biological molecular systems. Here, we introduce DEEP Picker, a deep neural network (DNN)-based approach for peak picking and spectral deconvolution which semi-automates the analysis of two-dimensional NMR spectra. DEEP Picker includes 8 hidden convolutional layers and was...
nmrlearner
Journal club
0
09-04-2021 10:34 AM
Students bring 'fresh insights' to scientific research on gene expression, deep neural networks and more - Clark University News Hub
http://www.bionmr.com//t1.gstatic.com/images?q=tbn:ANd9GcTVd062HSNkufpFLOXoHxhOr1s0onXKhPyi91bbXm51srwsuet1eajYCvbuLO7yooXH_P0TNwUX
Clark University News Hub
<img alt="" height="1" width="1">
Students bring 'fresh insights' to scientific research on gene expression, deep neural networks and more
Clark University News Hub
... biochemistry and molecular biology senior Pinky Htun '17 of Myanmar spent June and July isolating, purifying and studying proteins using state-of-the-art lab equipment, including a high-speed centrifuge and a nuclear magnetic resonance spectrometer.
Students...
nmrlearner
Online News
0
08-25-2016 05:42 AM
[NMR paper] Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins.
Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins.
Related Articles Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins.
Curr Opin Struct Biol. 2015 Apr 13;32:113-122
Authors: Kerfah R, Plevin MJ, Sounier R, Gans P, Boisbouvier J
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a uniquely powerful tool for studying the structure, dynamics and interactions of biomolecules at atomic resolution. In the past 15 years, the...
nmrlearner
Journal club
0
04-17-2015 08:49 PM
Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins
Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins
Publication date: June 2015
Source:Current Opinion in Structural Biology, Volume 32</br>
Author(s): Rime Kerfah , Michael J Plevin , Remy Sounier , Pierre Gans , Jerome Boisbouvier</br>
Nuclear magnetic resonance (NMR) spectroscopy is a uniquely powerful tool for studying the structure, dynamics and interactions of biomolecules at atomic resolution. In the past 15 years, the development of new isotopic labeling strategies has opened the possibility of exploiting...
nmrlearner
Journal club
0
04-14-2015 01:24 PM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins.
Related Articles Application of neural networks to automated assignment of NMR spectra of proteins.
J Biomol NMR. 1994 Jan;4(1):35-46
Authors: Hare BJ, Prestegard JH
Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
nmrlearner
Journal club
0
08-22-2010 03:33 AM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins.
Related Articles Application of neural networks to automated assignment of NMR spectra of proteins.
J Biomol NMR. 1994 Jan;4(1):35-46
Authors: Hare BJ, Prestegard JH
Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
nmrlearner
Journal club
0
08-22-2010 03:33 AM
High Resolution 1H Detected 1H,13C Correlation Spectra in MAS Solid-State NMR using Deuterated Proteins with Selective 1H,2H Isotopic Labeling of Methyl Groups
High Resolution <SUP>1</SUP>H Detected <SUP>1</SUP>H,<SUP>13</SUP>C Correlation Spectra in MAS Solid-State NMR using Deuterated Proteins with Selective <SUP>1</SUP>H,<SUP>2</SUP>H Isotopic Labeling of Methyl Groups
Vipin Agarwal, Anne Diehl, Nikolai Skrynnikov, and Bernd Reif
J. Am. Chem. Soc.; 2006; 128(39) pp 12620 - 12621;
Abstract:
MAS solid-state NMR experiments applied to biological solids are still hampered by low sensitivity and resolution. In this work, we employ a deuteration scheme in which individual methyl groups are selectively protonated. This labeling scheme...
Solution-state methyl NMR spectroscopy of large non-deuterated proteins enabled by deep neural networks
Linear Mode
