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 09-29-2016, 06:58 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,409
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 Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction

Acquiring and processing ultrafast biomolecular 2D NMR experiments using a referenced-based correction

Abstract

Thanks to their special spatiotemporal encoding/decoding scheme, ultrafast (UF) NMR sequences can deliver arbitrary 2D spectra following a single excitation. Regardless of their nature, these sequences have in common their tracing of a path in the \({\hbox {F}_{1}}\) â?? \(t_{2}\) plane, that will deliver the spectrum being sought after a 1D Fourier transformation versus \(t_{2}\) . This need to simultaneously digitize two domains, tends to impose bandwidth limitations along all spectral axes. Along the \(t_{2}\) / \({\hbox {F}_{2}}\) dimension this problem is exacerbated by the fact that odd and even time points are not equispaced, and by additional artifacts such as time shifts between time points sampled while under the action of positive and negative decoding gradients. As a result, odd and even \(t_{2}\) points are typically Fourier transformed separately, halving the potential spectral width along this dimension. While this halving of the \({\hbox {F}_{2}}\) span can be overcome by an interlaced Fourier transform, this post-processing is seldom used because of its sensitivity to hardware inaccuracies requiring even finer corrections of the even/odd \(t_{2}\) data points. These corrections have so far been done manually, but are challenging to implement when dealing with low signal-to-noise ratio signals like those associated with biomolecular NMR experiments. This study introduces an algorithm for an automatic correction of all even/odd ultrafast NMR inconsistencies, based on the acquisition of a reference scan on the solvent. This algorithm was verified experimentally using an \({}^{1}\hbox {H}\) - \({}^{13}\hbox {C}\) UF-HSQC variant on ubiquitin at 600Â*MHz. Features of this method as well as of the interlaced Fourier transformation in general, are discussed.



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] Applications of high dimensionality experiments to biomolecular NMR.
Applications of high dimensionality experiments to biomolecular NMR. Applications of high dimensionality experiments to biomolecular NMR. Prog Nucl Magn Reson Spectrosc. 2015 Nov;90-91:49-73 Authors: Nowakowski M, Saxena S, Stanek J, ?erko S, Ko?mi?ski W Abstract High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable...
nmrlearner Journal club 0 11-26-2015 12:13 AM
Applications of high dimensionality experiments to biomolecular NMR
Applications of high dimensionality experiments to biomolecular NMR Publication date: Available online 11 July 2015 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> Author(s): Micha? Nowakowski , Saurabh Saxena , Jan Stanek , Szymon ?erko , Wiktor Ko?mi?ski</br> High dimensionality NMR experiments facilitate resonance assignment and precise determination of spectral parameters such as coupling constants. Sparse non-uniform sampling enables acquisition of experiments of high dimensionality with high resolution in acceptable time. In this review...
nmrlearner Journal club 0 07-12-2015 07:12 AM
[NMR paper] A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions.
A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions. A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions. J Magn Reson. 2014 Nov 15;250C:37-44 Authors: Zhang R, Damron J, Vosegaard T, Ramamoorthy A Abstract Rotating-frame separated-local-field solid-state NMR experiments measure highly resolved heteronuclear dipolar couplings which, in turn, provide valuable interatomic distances for structural and dynamic studies...
nmrlearner Journal club 0 12-09-2014 01:13 PM
[NMR paper] Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.
Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations. Phys Chem Chem Phys. 2014 Jul 23; Authors: Zhu T, Zhang JZ, He X Abstract In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated...
nmrlearner Journal club 0 07-24-2014 11:56 AM
Correction for Li et al., Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion [Correction]
Correction for Li et al., Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion ... Date: 2013-11-26 BIOPHYSICS AND COMPUTATIONAL BIOLOGY Correction for “Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion,” by Ying Li, Nicole L. Altorelli, Fabiana Bahna, Barry Honig, Lawrence Shapiro, and Arthur G. Palmer III, which appeared in issue 41, October 8, 2013, of Proc Natl Acad Sci USA (110:16462–16467; first published September... Read More PNAS: Number: 48
nmrlearner Journal club 0 11-27-2013 01:50 AM
Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.
Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications. Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications. J Magn Reson. 2011 Apr;209(2):352-8 Authors: Shrot Y, Frydman L A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have...
nmrlearner Journal club 0 07-23-2011 08:54 AM
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution Abstract Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each...
nmrlearner Journal club 0 06-06-2011 12:53 AM
Correct mis-referenced NMR shifts with MANI-LACS
MANI-LACS Server v. 0.1 (Beta) MANI-LACS offers a new approach to NMR reference correction and outlier identification that achieves excellent results using only residue specific chemical shift assignment. http://bija.nmrfam.wisc.edu/MANI-LACS/seeds.jpg Instructions for preparing input files Database of chemical shift corrections
nmrlearner General 0 08-14-2005 09:11 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 - 2020, 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 11:12 PM.


Map