Related ArticlesResolving overlapped signals with automated FitNMR analytical peak modeling.
J Magn Reson. 2020 Jun 13;318:106773
Authors: Dudley JA, Park S, MacDonald ME, Fetene E, Smith CA
Abstract
Nuclear magnetic resonance (NMR) is a valuable tool for determining the structures of molecules and probing their dynamics. A longstanding problem facing both small-molecule and macromolecular NMR is overlapped signals in crowded spectra. To address this, we have developed a method that extracts peak features by fitting analytically derived models of NMR lineshapes. The approach takes into account the effects of truncation, apodization, and the resulting artifacts, while avoiding systematic errors that have affected other models. Even severely overlapped peaks, beyond the point of coalescence, can be distinguished in both simulated and experimental data. We show that the method can measure unresolved backbone scalar couplings directly from a 2D proton-nitrogen spectrum of a de novo designed mini protein. The algorithm is implemented in the FitNMR open-source R package and can be used to analyze nearly any type of single or multidimensional data from small molecules or biomolecules.
PMID: 32759043 [PubMed - as supplied by publisher]
[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] Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.
Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.
Related Articles Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.
J Biomol NMR. 2015 Oct 17;
Authors: Konuma T, Harada E, Sugase K
Abstract
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific...
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10-20-2015 09:44 PM
Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy
Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy
Abstract
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate...
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10-18-2015 09:10 AM
Peak height versus peak volume
Given a standard NOESY-based protein structure determination: Does anyone have any information on the benefits of measuring peak intensity by a volume integration method rather than simply measuring the peak height.
Obviously integration is theoretically more accurate, but does it make any difference to the quality of the structures produced? especially if peak lineshapes are comparable?
I was hoping to find some study comparing structures produced by both methods.....
I'm also curious about the benefits of distance-calbrating NOEs to a curve rather than simply putting restraints...
paul
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09-15-2015 07:48 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
Industrial Postdoctoral Chemist( analytical, organic or polymer) | Avomeen Analytical Services
Industrial Postdoctoral Chemist( analytical, organic or polymer) | Avomeen Analytical Services
US - Ann Arbor Michigan, Ph.D. in Analytical, organic or polymer chemistry. Hands-on knowledge of following techniques Analytical instrumentation is preferred: FT-IR, NMR, GC, GC-MS, LC-MS, TGA, DSC, ICP, and SEM-EDS. Must be
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12-19-2010 01:50 AM
[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...
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11-17-2010 11:15 PM
[NMR analysis blog] On integrating overlapped peaks
On integrating overlapped peaks
Following up from the integration problem raised in my previous post and before I delve into Line Fitting, I would like to give you a quick update on some progress we have recently done in Mnova to facilitate the accurate integration of peaks in those cases in which a multiplet is contaminated by one or several extraneous peaks (e.g. a solvent peak).
Consider the following spectrum predicted using NMRPredict Desktop
http://3.bp.blogspot.com/_-MfflvAgRls/S08KOThgdBI/AAAAAAAAAkU/RsKSptjbJ1g/s400/Integration1.jpg
As expected (this is a perfect synthetic...
Resolving overlapped signals with automated FitNMR analytical peak modeling.
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