BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 06-01-2017, 03:02 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,343
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Maximal clique method for the automated analysis of NMR TOCSY spectra of complex mixtures

Maximal clique method for the automated analysis of NMR TOCSY spectra of complex mixtures

Abstract

Characterization of the chemical components of complex mixtures in solution is important in many areas of biochemistry and chemical biology, including metabolomics. The use of 2D NMR total correlation spectroscopy (TOCSY) experiments has proven very useful for the identification of known metabolites as well as for the characterization of metabolites that are unknown by taking advantage of the good resolution and high sensitivity of this homonuclear experiment. Due to the complexity of the resulting spectra, automation is critical to facilitate and speed-up their analysis and enable high-throughput applications. To better meet these emerging needs, an automated spin-system identification algorithm of TOCSY spectra is introduced that represents the cross-peaks and their connectivities as a mathematical graph, for which all subgraphs are determined that are maximal cliques. Each maximal clique can be assigned to an individual spin system thereby providing a robust deconvolution of the original spectrum for the easy extraction of critical spin system information. The approach is demonstrated for a complex metabolite mixture consisting of 20 compounds and for E. coli cell lysate.



Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] A NMR reverse diffusion filter for the simplification of spectra of complex mixtures and the study of drug receptor interactions.
A NMR reverse diffusion filter for the simplification of spectra of complex mixtures and the study of drug receptor interactions. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary_FullTextOnline_120x27.gif Related Articles A NMR reverse diffusion filter for the simplification of spectra of complex mixtures and the study of drug receptor interactions. Magn Reson Chem. 2011 Aug;49(8):464-8 Authors: Vega-Vázquez M, Cobas JC, Oliveira de Sousa FF, Martin-Pastor M ...
nmrlearner Journal club 0 07-01-2015 02:40 PM
Quantitative Trace Analysis of Complex Mixtures Using SABRE Hyperpolarization
From The DNP-NMR Blog: Quantitative Trace Analysis of Complex Mixtures Using SABRE Hyperpolarization Eshuis, N., et al., Quantitative Trace Analysis of Complex Mixtures Using SABRE Hyperpolarization. Angew Chem Int Ed Engl, 2014: p. n/a-n/a. http://www.ncbi.nlm.nih.gov/pubmed/25469822
nmrlearner News from NMR blogs 0 01-12-2015 11:31 PM
[NMR paper] Quantitative Quantum Mechanical Spectral Analysis (qQMSA) of (1)H NMR spectra of complex mixtures and biofluids.
Quantitative Quantum Mechanical Spectral Analysis (qQMSA) of (1)H NMR spectra of complex mixtures and biofluids. Related Articles Quantitative Quantum Mechanical Spectral Analysis (qQMSA) of (1)H NMR spectra of complex mixtures and biofluids. J Magn Reson. 2014 Feb 18;242C:67-78 Authors: Tiainen M, Soininen P, Laatikainen R Abstract The quantitative interpretation of (1)H NMR spectra of mixtures like the biofluids is a demanding task due to spectral complexity and overlap. Complications may arise also from water suppression, T2-editing,...
nmrlearner Journal club 0 03-14-2014 06:40 AM
[NMR paper] Quantitative Quantum Mechanical Spectral Analysis (qQMSA) of 1H NMR Spectra of Complex Mixtures and Biofluids
Quantitative Quantum Mechanical Spectral Analysis (qQMSA) of 1H NMR Spectra of Complex Mixtures and Biofluids Publication date: Available online 18 February 2014 Source:Journal of Magnetic Resonance</br> Author(s): Mika Tiainen , Pasi Soininen , Reino Laatikainen</br> The quantitative interpretation of 1H NMR spectra of mixtures like the biofluids is a demanding task due to spectral complexity and overlap. Complications may arise also from water suppression, T2-editing, protein interactions, relaxation differences of the species, experimental artifacts and,...
nmrlearner Journal club 0 02-19-2014 03:12 PM
Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics
Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics November 2011 Publication year: 2011 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 4</br> </br> Highlights
nmrlearner Journal club 0 12-15-2012 09:51 AM
Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics
Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics Publication year: 2011 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 4</br> James S. McKenzie, James A. Donarski, Julie C. Wilson, Adrian J. Charlton</br> </br> </br></br>
nmrlearner Journal club 0 03-09-2012 09:16 AM
Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics
Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics Publication year: 2011 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 12 May 2011</br> James S., McKenzie , James A., Donarski , Julie C., Wilson , Adrian J., Charlton</br> *Highlights:*? Analysis of complex mixtures using NMR spectroscopy. ? Use of chemometrics for interpretation of spectra. ? Review of sample handling approaches. ? Discussion of spectral processing methods. ? Discussion of supervised and...
nmrlearner Journal club 0 05-13-2011 07:41 AM
[NMR paper] Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). Related Articles Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J Biomol NMR. 2002 Aug;23(4):271-87 Authors: Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR Automated assignment of NOESY spectra is a prerequisite for automated structure determination of biological macromolecules. With the program KNOWNOE we present a novel, knowledge based approach to this problem. KNOWNOE...
nmrlearner Journal club 0 11-24-2010 08:58 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2018, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 10:50 AM.


Map