NMR paper Automated peak picking and peak integration in macromolecular NMR spectra using AUTOP

		BioNMR > Educational resources > Journal club
[NMR paper] Automated peak picking and peak integration in macromolecular NMR spectra using AUTOP

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-17-2010, 11:15 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Automated peak picking and peak integration in macromolecular NMR spectra using AUTOP

Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY.

Related Articles Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY.

J Magn Reson. 1998 Dec;135(2):288-97

Authors: Koradi R, Billeter M, Engeli M, Güntert P, Wüthrich K

A new approach for automated peak picking of multidimensional protein NMR spectra with strong overlap is introduced, which makes use of the program AUTOPSY (automated peak picking for NMR spectroscopy). The main elements of this program are a novel function for local noise level calculation, the use of symmetry considerations, and the use of lineshapes extracted from well-separated peaks for resolving groups of strongly overlapping peaks. The algorithm generates peak lists with precise chemical shift and integral intensities, and a reliability measure for the recognition of each peak. The results of automated peak picking of NOESY spectra with AUTOPSY were tested in combination with the combined automated NOESY cross peak assignment and structure calculation routine NOAH implemented in the program DYANA. The quality of the resulting structures was found to be comparable with those from corresponding data obtained with manual peak picking.

PMID: 9878459 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Peak height versus peak volume Given a standard NOESY-based protein structure determination: Does anyone have any information on the benefits of measuring peak intensity by a volume integration method rather than simply measuring the peak height. Obviously integration is theoretically more accurate, but does it make any difference to the quality of the structures produced? especially if peak lineshapes are comparable? I was hoping to find some study comparing structures produced by both methods..... I'm also curious about the benefits of distance-calbrating NOEs to a curve rather than simply putting restraints...	paul	NMR Questions and Answers	3	09-15-2015 07:48 PM
[Question from NMRWiki Q&A forum] Auto peak picking of N15Edit NOESY and C13 Edit NOESY spectrum Auto peak picking of N15Edit NOESY and C13 Edit NOESY spectrum Dear friends, I am in process of doing structure calculation of a dimeric protein. The problem I faced is regarding the assignment of N15Edit NOESY and C13 Edit NOESY spectrum.I have already processed the fid data and converted to sparky ucsf format. Is there options available in sparky for auto peak picking, integration and assignment of my NOESY spectrum? And second query is regarding the generation of input files for structure calculation. In our Lab we are using ARIA 2.1 software for structure calculation? Is there any...	nmrlearner	News from other NMR forums	0	12-14-2011 07:14 PM
[NMRpipe Yahoo group] nmrpipe peak picking simplified nmrpipe peak picking simplified Hi everybody I am trying to simplify my assignment process: For this I would like to use a 2D projection from a 3D NOESY where I can easily pick and assign and More...	NMRpipe Yahoo group news	News from other NMR forums	0	09-23-2011 05:53 AM
[NMRpipe Yahoo group] Problem peak-picking 3D spectra Problem peak-picking 3D spectra Hello All, I've been trying to run the automated peak detection, but I've run into some difficulty. Picking a slice from a 3D spectrum works without problems, More...	NMRpipe Yahoo group news	News from other NMR forums	0	05-27-2011 10:40 AM
[NMR analysis blog] Intelligent Peak Picking of 1D NMR Spectra Intelligent Peak Picking of 1D NMR Spectra In case you hadn´t noticed, version 7 of Mnova was released just a few days ago. Whilst this new version presents a number of significant improvements in the software, in this post I would like to focus on a new peak picking concept which, to the best of my knowledge, is novel and in some way, revolutionary. I will try to keep this as short and clear as possible, just to illustrate the very basic ideas that motivated this new approach to peak picking. In the next posts I will elaborate further on some of the new points introduced here. ...	nmrlearner	News from NMR blogs	0	05-16-2011 08:23 PM
[NMR Sparky Yahoo group] peak color peak color Is there a way to edit the some file so that every time i pick a peak and label it so that they come up black instead of white? More...	nmrlearner	News from other NMR forums	0	10-29-2010 09:32 PM
Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm John J. Kuszewski, Robin Augustine Thottungal, G. Marius Clore and Charles D. Schwieters Journal of Biomolecular NMR; 2008; 41(4); pp 221-239 Abstract: We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258–6273). The improved protocol includes...	Abe	Journal club	0	09-21-2008 11:43 PM

« Previous Thread | Next 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