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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 02-06-2016, 03:10 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
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 Non-uniform sampling of NMR relaxation data.

Non-uniform sampling of NMR relaxation data.

Related Articles Non-uniform sampling of NMR relaxation data.

J Biomol NMR. 2016 Feb 4;

Authors: Linnet TE, Teilum K

Abstract
The use of non-uniform sampling of NMR spectra may give significant reductions in the data acquisition time. For quantitative experiments such as the measurement of spin relaxation rates, non-uniform sampling is however not widely used as inaccuracies in peak intensities may lead to errors in the extracted dynamic parameters. By systematic reducing the coverage of the Nyquist grid of (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion datasets for four different proteins and performing a full data analysis of the resulting non-uniform sampled datasets, we have compared the performance of the multi-dimensional decomposition and iterative re-weighted least-squares algorithms in reconstructing spectra with accurate peak intensities. As long as a single fully sampled spectrum is included in a series of otherwise non-uniform sampled two-dimensional spectra, multi-dimensional decomposition reconstructs the non-uniform sampled spectra with high accuracy. For two of the four analyzed datasets, a coverage of only 20*% results in essentially the same results as the fully sampled data. As exemplified by other data, such a low coverage is in general not enough to produce reliable results. We find that a coverage level not compromising the final results can be estimated by recording a single full two-dimensional spectrum and reducing the spectrum quality in silico.


PMID: 26847574 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Non-uniform sampling of NMR relaxation data
Non-uniform sampling of NMR relaxation data Abstract The use of non-uniform sampling of NMR spectra may give significant reductions in the data acquisition time. For quantitative experiments such as the measurement of spin relaxation rates, non-uniform sampling is however not widely used as inaccuracies in peak intensities may lead to errors in the extracted dynamic parameters. By systematic reducing the coverage of the Nyquist grid of 15N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion datasets for four different proteins and performing a full...
nmrlearner Journal club 0 02-05-2016 02:38 PM
[NMR paper] Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.
Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination. Related Articles Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination. Chemistry. 2015 Jul 28; Authors: Didenko T, Proudfoot A, Dutta SK, Serrano P, Wüthrich K Abstract High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments...
nmrlearner Journal club 0 08-02-2015 07:10 AM
[NMR paper] Performance tuning non-uniform sampling for sensitivity enhancement of signal-limited biological NMR.
Performance tuning non-uniform sampling for sensitivity enhancement of signal-limited biological NMR. Related Articles Performance tuning non-uniform sampling for sensitivity enhancement of signal-limited biological NMR. J Biomol NMR. 2014 Mar 29; Authors: Palmer MR, Wenrich BR, Stahlfeld P, Rovnyak D Abstract Non-uniform sampling (NUS) has been established as a route to obtaining true sensitivity enhancements when recording indirect dimensions of decaying signals in the same total experimental time as traditional uniform...
nmrlearner Journal club 0 04-01-2014 02:47 PM
[NMR paper] Time-resolved multidimensional NMR with non-uniform sampling.
Time-resolved multidimensional NMR with non-uniform sampling. Time-resolved multidimensional NMR with non-uniform sampling. J Biomol NMR. 2014 Jan 17; Authors: Mayzel M, Rosenlöw J, Isaksson L, Orekhov VY Abstract Time-resolved experiments demand high resolution both in spectral dimensions and in time of the studied kinetic process. The latter requirement traditionally prohibits applications of the multidimensional experiments, which, although capable of providing invaluable information about structure and dynamics and almost unlimited...
nmrlearner Journal club 0 01-18-2014 11:31 AM
[NMR analysis blog] Non Uniform Sampling (NUS) NMR Processing
Non Uniform Sampling (NUS) NMR Processing Background In the last few years, Non-Uniform Sampling (NUS) has emerged as a very powerful tool to significantly speed up the acquisition of multidimensional NMR experiments due to the fact that only a subset of the usual linearly sampled data in the Nyquist grid is measured. Unfortunately, this fast acquisition modality introduces a new challenge as the normal Fourier Transform will fail and consequently, special processing techniques are required. A number of sophisticated methods have been proposed for reconstructing sparsely sampled 2D...
nmrlearner News from NMR blogs 0 12-21-2013 03:15 PM
An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR
An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR June 2012 Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 219</br> </br> Non-uniform weighted sampling (NUWS) is a sampling strategy, related to non-uniform sampling (NUS) in the limit of long acquisition times, in which each indirect increment of a multidimensional spectrum is sampled multiple times according to some weighting function. As the spectrum is fully sampled it can be processed in a conventional manner by the...
nmrlearner Journal club 0 02-03-2013 10:13 AM
[NMRpipe Yahoo group] Re: extraction of 2D data according to non linear sampling schedule
Re: extraction of 2D data according to non linear sampling schedule Dear all£¬ I met the same condition as Ratan posted two years ago.Is there anyone have tips? Thanks in advance. tang More...
NMRpipe Yahoo group news News from other NMR forums 0 06-28-2012 07:54 AM
An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR
An analysis of NMR sensitivity enhancements obtained using non-uniform weighted sampling, and the application to protein NMR Publication year: 2012 Source:Journal of Magnetic Resonance</br> Christopher A. Waudby, John Christodoulou</br> Non-uniform weighted sampling (NUWS) is a sampling strategy, related to non-uniform sampling (NUS) in the limit of long acquisition times, in which each indirect increment of a multidimensional spectrum is sampled multiple times according to some weighting function. As the spectrum is fully sampled it can be processed in a conventional...
nmrlearner Journal club 0 05-01-2012 08:03 PM



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 - 2024, 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 02:36 PM.


Map