Rapid progress in machine learning offers new opportunities for the automated analysis of multidimensional NMR spectra ranging from protein NMR to metabolomics applications. Most recently, it has been demonstrated how deep neural networks (DNN) designed for spectral peak picking are capable of deconvoluting highly crowded NMR spectra rivaling the facilities of human experts. Superior DNN-based peak picking is one of a series of critical steps during NMR spectral processing, analysis, and interpretation where machine learning is expected to have a major impact. In this perspective, we lay out some of the unique strengths as well as challenges of machine learning approaches in this new era of automated NMR spectral analysis. Such a discussion seems timely and should help define common goals for the NMR community, the sharing of software tools, standardization of protocols, and calibrate expectations. It will also help prepare for an NMR future where machine learning and artificial intelligence tools will be common place.
[NMR paper] NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.
NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.
NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.
Bioinformatics. 2018 Mar 14;:
Authors: Klukowski P, Augoff M, Zieba M, Drwal M, Gonczarek A, Walczak MJ
Abstract
Motivation: Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would...
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03-17-2018 12:12 PM
[NMR paper] Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK.
Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK.
Related Articles Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK.
J Biomol NMR. 2017 Feb 03;:
Authors: Würz JM, Güntert P
Abstract
The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK,...
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02-06-2017 11:28 AM
Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK
Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK
Abstract
The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection...
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02-03-2017 09:55 PM
[NMR paper] Computer Vision - Based Automated Peak Picking Applied to Protein NMR Spectra.
Computer Vision - Based Automated Peak Picking Applied to Protein NMR Spectra.
Related Articles Computer Vision - Based Automated Peak Picking Applied to Protein NMR Spectra.
Bioinformatics. 2015 May 20;
Authors: Klukowski P, Walczak MJ, Gonczarek A, Boudet J, Wider G
Abstract
MOTIVATION: A detailed analysis of multidimensional NMR spectra of macromolecules requires the identification of individual resonances (peaks). This task can be tedious and time-consuming and often requires support by experienced users. Automated peak...
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05-23-2015 10:08 AM
[NMR paper] Bayesian Peak Picking for NMR Spectra.
Bayesian Peak Picking for NMR Spectra.
Related Articles Bayesian Peak Picking for NMR Spectra.
Genomics Proteomics Bioinformatics. 2013 Oct 31;
Authors: Cheng Y, Gao X, Liang F
Abstract
Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein-DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This...
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11-05-2013 06:53 PM
[NMRpipe Yahoo group] Problem peak-picking 3D spectra
Problem peak-picking 3D spectra
Hello All, I've been trying to run the automated peak detection, but I've run into some difficulty. Picking a slice from a 3D spectrum works without problems,
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05-27-2011 10:40 AM
[NMR analysis blog] Intelligent Peak Picking of 1D NMR Spectra
Intelligent Peak Picking of 1D NMR Spectra
In case you hadn´t noticed, version 7 of Mnova was released just a few days ago.
Whilst this new version presents a number of significant improvements in the software, in this post I would like to focus on a new peak picking concept which, to the best of my knowledge, is novel and in some way, revolutionary. I will try to keep this as short and clear as possible, just to illustrate the very basic ideas that motivated this new approach to peak picking. In the next posts I will elaborate further on some of the new points introduced here.
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05-16-2011 08:23 PM
[NMR paper] Automated peak picking and peak integration in macromolecular NMR spectra using AUTOP
Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY.
Related Articles Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY.
J Magn Reson. 1998 Dec;135(2):288-97
Authors: Koradi R, Billeter M, Engeli M, Güntert P, Wüthrich K
A new approach for automated peak picking of multidimensional protein NMR spectra with strong overlap is introduced, which makes use of the program AUTOPSY (automated peak picking for NMR spectroscopy). The main elements of this program are a novel...
Fundamental and practical aspects of machine learning for the peak picking of biomolecular NMR spectra
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