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  
Unread 09-29-2005, 04:33 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,178
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

Multiway Decomposition of NMR Spectra with Coupled Evolution Periods
Daniel Malmodin and Martin Billeter
J. Am. Chem. Soc.; 2005; 127(39), pp 13486 - 13487




Abstract:

Coupling evolution periods in NMR experiments on proteins has recently attracted much attention for its substantial savings in measurement time. Using the concept of multiway decomposition, which already proved useful in many types of NMR applications, the novel tool PRODECOMP decomposes sets of spectra with coupled evolution periods and attempts to provide all information that would be found in a corresponding full-dimensional spectrum. It offers the following advantages: (1) all experimental spectra are used simultaneously, avoiding sensitivity loss associated with individual examination of the spectra, (2) folding (aliasing) caused by the linear combinations of individual shifts in the projected spectra is automatically resolved, allowing for better resolution due to smaller spectral widths, (3) various types of schemes for the coupling of evolution periods are possible, (4) reconstructions of various high-dimensional spectra, including the corresponding full-dimensional spectrum, are straightforward, (5) overlap in both the projected and the directly detected dimensions is efficiently resolved. The capabilities of PRODECOMP are illustrated for a 14 kD protein, for which 12 projections of a five-dimensional spectrum with the nuclei N, HN, CO, C, and H are analyzed.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Structural Characterisation of a Histone Domain by Projection-Decomposition
Structural Characterisation of a Histone Domain by Projection-Decomposition Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 23 February 2012</br> Jonas*Fredriksson, Wolfgang*Bermel, Martin*Billeter</br> We demonstrate that two projection experiments, aN-HSQC–NOESY–N-HSQC and aC-HSQC–NOESY–N-HSQC, recorded for a histone domain from yeast, contain enough information to support a structural characterisation of the protein. At the temperature used, 298K, the histone domain exhibits a very high extent of chemical shift degeneracy that is uncharacteristic for...
nmrlearner Journal club 0 02-25-2012 04:20 PM
AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra
AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra Publication year: 2011 Source: Journal of Magnetic Resonance, Available online 8 October 2011</br> Ye*Tian, Charles D.*Schwieters, Stanley J.*Opella, Francesca M.*Marassi</br> AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between...
nmrlearner Journal club 0 10-10-2011 06:27 AM
Analysis of non-uniformly sampled spectra with Multi-Dimensional Decomposition
Analysis of non-uniformly sampled spectra with Multi-Dimensional Decomposition Publication year: 2011 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 24 February 2011</br> Vladislav Yu., Orekhov , Victor A., Jaravine</br> More...
nmrlearner Journal club 0 02-26-2011 01:07 PM
[NMR paper] Signal identification in NMR spectra with coupled evolution periods.
Signal identification in NMR spectra with coupled evolution periods. Related Articles Signal identification in NMR spectra with coupled evolution periods. J Magn Reson. 2005 Sep;176(1):47-53 Authors: Malmodin D, Billeter M Novel multidimensional NMR experiments rely on modified time-domain sampling schemes to provide significant savings of experimental time. Several approaches are based on the coupling of evolution times resulting in a reduction of the dimensionality of the recorded spectra, and a concomitant saving of experimental time. We...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Accuracy and robustness of three-way decomposition applied to NMR data.
Accuracy and robustness of three-way decomposition applied to NMR data. Related Articles Accuracy and robustness of three-way decomposition applied to NMR data. J Magn Reson. 2005 Jun;174(2):188-99 Authors: Luan T, Orekhov VY, Gutmanas A, Billeter M Three-way decomposition is a very versatile analysis tool with applications in a variety of protein NMR fields. It has been used to extract structural data from 3D NOESYs, to determine relaxation rates in large proteins, to identify ligand binding in screening for lead compounds, and to complement...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Optimizing resolution in multidimensional NMR by three-way decomposition.
Optimizing resolution in multidimensional NMR by three-way decomposition. Related Articles Optimizing resolution in multidimensional NMR by three-way decomposition. J Biomol NMR. 2003 Oct;27(2):165-73 Authors: Orekhov VY, Ibraghimov I, Billeter M Resolution depends on the number of points sampled in a FID; in indirectly detected dimensions it is an important determinant of the total experiment time. Based on the high redundancy present in NMR data, we propose the following timesaving scheme for three-dimensional spectra. An extensive grid of...
nmrlearner Journal club 0 11-24-2010 09:16 PM
Improved Resolution in Dipolar NMR Spectra Using Constant Time Evolution PISEMA Exper
Improved Resolution in Dipolar NMR Spectra Using Constant Time Evolution PISEMA Experiment. Related Articles Improved Resolution in Dipolar NMR Spectra Using Constant Time Evolution PISEMA Experiment. Chem Phys Lett. 2010 Jul 9;494(1-3):104-110 Authors: Gopinath T, Veglia G The atomic structure of small molecules and polypeptides can be attained from anisotropic NMR parameters such as dipolar couplings (DC) and chemical shifts (CS). Separated local field experiments resolve DC and CS correlations into two dimensions. However, crowded NMR...
nmrlearner Journal club 0 09-05-2010 05:53 AM
How to process ZQ evolution in the indirect dimension
I want process ZQ evolution in the indirect dimension. In Professor Pervushin's paper(Proc. Natl. Acad. Sci. USA Vol. 96, pp. 9607–9612, August 1999). He has mentioned "After Fourier transformation in the w2 dimension, the complex interferogram is multiplied by exp, where wh is the offset in the w2 dimension relative to the 1H carrier frequency in rad/s." Can anyone tell me the detail.
rogeryao NMR Questions and Answers 0 08-16-2006 03:32 AM



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 12:41 AM.


Map