Descriptive review of current NMR-based metabolomic data analysis packages

		BioNMR > Educational resources > Journal club
Descriptive review of current NMR-based metabolomic data analysis packages

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

12-15-2012, 09:51 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

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

Descriptive review of current NMR-based metabolomic data analysis packages

Descriptive review of current NMR-based metabolomic data analysis packages

October 2011
Publication year: 2011
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 3

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Descriptive review of current NMR-based metabolomic data analysis packages Descriptive review of current NMR-based metabolomic data analysis packages October 2011 Publication year: 2011 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 3</br> </br> </br> </br></br>	nmrlearner	Journal club	0	12-01-2012 06:10 PM
Descriptive review of current NMR-based metabolomic data analysis packages Descriptive review of current NMR-based metabolomic data analysis packages Publication year: 2011 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 3</br> Jose L. Izquierdo-García, Palmira Villa, Angelos Kyriazis, Laura del Puerto-Nevado, Sandra Pérez-Rial, Ignacio Rodriguez, Natalia Hernandez, Jesús Ruiz-Cabello</br> </br> </br></br>	nmrlearner	Journal club	0	03-09-2012 09:16 AM
Use of optimized 1D TOCSY NMR for improved quantitation and metabolomic analysis of biofluids Use of optimized 1D TOCSY NMR for improved quantitation and metabolomic analysis of biofluids Abstract One dimensional selective TOCSY experiments have been shown to be advantageous in providing improved data inputs for principle component analysis (PCA) (Sandusky and Raftery 2005a, b). Better subpopulation cluster resolution in the observed scores plots results from the ability to isolate metabolite signals of interest via the TOCSY based filtering approach. This report reexamines the quantitative aspects of this approach, first by optimizing the 1D TOCSY experiment as it relates to...	nmrlearner	Journal club	0	03-13-2011 05:24 AM
Descriptive Review of Current NMR-Based Metabolomic Data Analysis Packages Descriptive Review of Current NMR-Based Metabolomic Data Analysis Packages Publication year: 2011 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 21 February 2011</br> Jose L., Izquierdo-García , Palmira, Villa , Angelos, Kyriazis , Laura del, Puerto-Nevado , Sandra, Pérez-Rial , ...</br> More...	nmrlearner	Journal club	0	02-22-2011 11:00 AM
A NMR-based metabolomic approach for differentiation of hagfish dental and somatic skeletal muscles. A NMR-based metabolomic approach for differentiation of hagfish dental and somatic skeletal muscles. A NMR-based metabolomic approach for differentiation of hagfish dental and somatic skeletal muscles. Fish Physiol Biochem. 2011 Feb 15; Authors: Chiu KH, Ding S, Chen YW, Lee CH, Mok HK The hagfish dental muscle is a large and specialized element of the feeding apparatus that helps ingest food. This muscle has enzymatic activities and contractile properties different from the hagfish somatic skeletal muscle. To verify the functional relevance of...	nmrlearner	Journal club	0	02-18-2011 08:07 PM
[NMR tweet] UCL Research: High resolution 1H nuclear magnetic resonance spectroscopic-based metabolomic urine analysis of ex... http://bit.ly/f8UR1h UCL Research: High resolution 1H nuclear magnetic resonance spectroscopic-based metabolomic urine analysis of ex... http://bit.ly/f8UR1h Published by ucl_discovery (UCL Discovery) on 2010-12-16T07:44:35Z Source: Twitter	nmrlearner	Twitter NMR	0	12-16-2010 07:45 AM
(1)H-NMR-based metabolomic study on resistance to diet-induced obesity in AHNAK knock (1)H-NMR-based metabolomic study on resistance to diet-induced obesity in AHNAK knock-out mice. (1)H-NMR-based metabolomic study on resistance to diet-induced obesity in AHNAK knock-out mice. Biochem Biophys Res Commun. 2010 Nov 18; Authors: Kim IY, Jung J, Jang M, Ahn YG, Shin JH, Choi JW, Sohn MR, Shin SM, Kang DG, Lee HS, Bae YS, Ryu DH, Seong JK, Hwang GS AHNAK is a giant protein of approximately 700 kD identified in human neuroblastomas and skin epithelial cells. Recently, we found that AHNAK knock-out (AHNAK(-/-)) mice have a strong...	nmrlearner	Journal club	0	11-26-2010 05:32 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