Question from NMRWiki Q&A forum How to plot chemical shift predictions obtained form SPARTA?

		BioNMR > NMR community > News from other NMR forums
[Question from NMRWiki Q&A forum] How to plot chemical shift predictions obtained form SPARTA?

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

11-18-2010, 06:16 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

How to plot chemical shift predictions obtained form SPARTA?

How to plot chemical shift predictions obtained form SPARTA?

Dear friends,

I had a mutation in my protein and now I have some amino acids around mutation remained unassigned. To get a way to find the missing peaks I modelled the mutated protein with modeller and out of the pdb file I got the chemical shift predictions using SPARTA. Now that I have chemical shift predictions I want to plot them like a spectra and overlay them to my real spectra to see if it will help me to assign some of the missing peaks. I know for solid-state NMR there is a software, but what about solution NMR?

Looking forward to hearing from you.

Thanks!Mahnaz

Check if somebody has answered this question on NMRWiki QA forum

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
SHIFTX2: Chemical Shift Prediction SHIFTX2 website SHIFTX2 is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain...	gwnmr	NMR software	0	01-10-2012 06:13 PM
[NMR tweet] RT @ScienceNews24: Nuclear magnetic resonance (NMR) is a powerful tool for chemical analysis and, in the form of magnetic resonan... http://zmarter.com/2016257 RT @ScienceNews24: Nuclear magnetic resonance (NMR) is a powerful tool for chemical analysis and, in the form of magnetic resonan... http://zmarter.com/2016257 Published by aladinsain (Daran Stebbing) on 2011-05-18T10:06:16Z Source: Twitter	nmrlearner	Twitter NMR	0	05-18-2011 10:30 AM
[Question from NMRWiki Q&A forum] NutsPro software to extract a plot from a stacked plot file NutsPro software to extract a plot from a stacked plot file Hello, I was using VnmrJ to collect an array of 6 NMR spectra. I used VnmrJ to save all 6 spectra in 1 fid file by using the svf('filename') command. When opening the fid file in NutsPro to analyze the data, I am able to see all 6 spectra in Stacked Plots mode. They show up as Fid spectra, stacked on top of each other. However I am only able to individually display the first plot and only able to take the Fourier Transform of that first plot in the series. I am unable to select any other plot in that array. Is there a way in...	nmrlearner	News from other NMR forums	0	03-04-2011 02:12 AM
Chapter 13 - NMR Chemical Shift Chapter 13 - NMR Chemical Shift More...	nmrlearner	NMR bookmarks	0	08-19-2010 02:34 PM
ChemSpider - Database of Chemical Structures and Property Predictions ChemSpider - Database of Chemical Structures and Property Predictions More...	nmrlearner	NMR bookmarks	0	08-19-2010 02:34 PM
SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of Abstract NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13CÎ² chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures,...	nmrlearner	Journal club	0	08-14-2010 04:19 AM
Chemical shift of protons? Can someone give me the answers to the chemical shift of the protons in this compound: CH3CH2OCH2CH(CH3)COOH? Of if you can explain how to get the chemical shift it would be quite helpful as the info online does not really help me.	Tim Mrudande	NMR Questions and Answers	1	01-16-2005 08:23 AM
what is/ how do you calculate the chemical shift in an NMR? I have read the technical definitions but I still do not understand what the chemical shift means and how you calculate it given an NMR peak. If someone could kind of dumb it down for me but still give me the important things to know/ how it helps you determine the structure of a molecule with the NMR I would appreciate it.	Courtney	NMR Questions and Answers	1	01-01-2002 06:47 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