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 11-19-2010, 08:44 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,700
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 Potential bias in NMR relaxation data introduced by peak intensity analysis and curve

Potential bias in NMR relaxation data introduced by peak intensity analysis and curve fitting methods.

Related Articles Potential bias in NMR relaxation data introduced by peak intensity analysis and curve fitting methods.

J Biomol NMR. 2001 Sep;21(1):1-9

Authors: Viles JH, Duggan BM, Zaborowski E, Schwarzinger S, Huntley JJ, Kroon GJ, Dyson HJ, Wright PE

We present an evaluation of the accuracy and precision of relaxation rates calculated using a variety of methods, applied to data sets obtained for several very different protein systems. We show that common methods of data evaluation, such as the determination of peak heights and peak volumes, may be subject to bias, giving incorrect values for quantities such as R1 and R2. For example, one common method of peak-height determination, using a search routine to obtain the peak-height maximum in successive spectra, may be a source of significant systematic error in the relaxation rate. The alternative use of peak volumes or of a fixed coordinate position for the peak height in successive spectra gives more accurate results, particularly in cases where the signal/noise is low, but these methods have inherent problems of their own. For example, volumes are difficult to quantitate for overlapped peaks. We show that with any method of sampling the peak intensity, the choice of a 2- or 3-parameter equation to fit the exponential relaxation decay curves can dramatically affect both the accuracy and precision of the calculated relaxation rates. In general, a 2-parameter fit of relaxation decay curves is preferable. However, for very low intensity peaks a 3 parameter fit may be more appropriate.

PMID: 11693564 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins Abstract Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was...
nmrlearner Journal club 0 06-06-2011 12:53 AM
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins. relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins. J Biomol NMR. 2011 May 27; Authors: Bieri M, d'Auvergne EJ, Gooley PR Investigation of protein dynamics on the ps-ns and ?s-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying...
nmrlearner Journal club 0 05-28-2011 06:50 PM
[NMR paper] Analysis of slow interdomain motion of macromolecules using NMR relaxation data.
Analysis of slow interdomain motion of macromolecules using NMR relaxation data. Related Articles Analysis of slow interdomain motion of macromolecules using NMR relaxation data. J Am Chem Soc. 2001 May 2;123(17):3953-9 Authors: Baber JL, Szabo A, Tjandra N The interpretation of NMR relaxation data for macromolecules possessing slow interdomain motions is considered. It is shown how the "extended model-free approach" can be used to analyze (15)N backbone relaxation data acquired at three different field strengths for Xenopus Ca(2+)-ligated...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMRwiki tweet] nmrwiki: How is peak intensity related to J coupling in COSY? #nmrhttp://qa.nmrwiki.o
nmrwiki: How is peak intensity related to J coupling in COSY? #nmrhttp://qa.nmrwiki.org/question/197/ nmrwiki: How is peak intensity related to J coupling in COSY? #nmrhttp://qa.nmrwiki.org/question/197/ Source: NMRWiki tweets
nmrlearner Twitter NMR 0 11-18-2010 06:16 PM
[Question from NMRWiki Q&A forum] What software can copy peak assignments for 2D T1 and T2 relaxation rate data analysi
What software can copy peak assignments for 2D T1 and T2 relaxation rate data analysis? Hello, I'm currently processing a large amount of T1 and T2 spectra in NMRDraw. I've been looking for a way to copy my peak assignments from one spectrum onto to the others so that I can quickly and accurately match height and volume values, but I've had little luck so far. Is it possible to manipulate the assignment tables to achieve this goal? NMRPipe and its associated applications are all very new to me at this point, so any information that may expand my general knowledge of the program or...
nmrlearner News from other NMR forums 0 08-22-2010 02:30 AM
[NMR paper] Assessing potential bias in the determination of rotational correlation times of prot
Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation. Related Articles Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation. J Biomol NMR. 1999 Feb;13(2):101-12 Authors: Lee AL, Wand AJ The various factors that influence the reliable and efficient determination of the correlation time describing molecular reorientation of proteins by NMR relaxation methods are examined. Nuclear Overhauser effects, spin-lattice, and spin-spin relaxation...
nmrlearner Journal club 0 08-21-2010 04:03 PM
peak intensity vs number of scans
Hi, I have a question regarding how the peak intensities change when with increase in number of scans when the data is collected on a Varian NMR spectrometer. Suppose I collect a 15N-1H HSQC spectra with 8 scans and then collect the same spectra with 16 scans, would the peak intensities be double in the 16 scan spectra as compared to the 8 scan spectra? Does anyone know how the varian spectrometer scales the intensities according to the number of scans? Any suggestion or reply to my query will be extremely useful and greatly appreciated. Thanks.
aish1982 NMR software 0 08-08-2008 11:56 PM
peak intensity vs number of scans
Hi, I have a question regarding how the peak intensities change when with increase in number of scans when the data is collected on a Varian NMR spectrometer. Suppose I collect a 15N-1H HSQC spectra with 8 scans and then collect the same spectra with 16 scans, would the peak intensities be double in the 16 scan spectra as compared to the 8 scan spectra? Does anyone know how the varian spectrometer scales the intensities according to the number of scans? Any suggestion or reply to my query will be extremely useful and greatly appreciated. Thanks.
aish1982 NMR Questions and Answers 0 08-08-2008 07:28 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 02:54 PM.


Map