BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > NMR community > NMR pictures
Advanced Search



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 12-20-2011, 04:09 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Alignment of NMR spectra ? The


http://nmr-analysis.blogspot.com/201...em-part-i.html
20/12/2011 4:11:50 PM GMT
Alignment of NMR spectra ? The
More...
Reply With Quote

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR analysis blog] Alignment of NMR spectra – Part VI: Reaction Monitoring (II)
Alignment of NMR spectra – Part VI: Reaction Monitoring (II) Previous posts on this series: Alignment of NMR spectra – Part I: The problem Alignment of NMR spectra – Part II: Binning / Bucketing Alignment of NMR spectra – Part III: Global Alignment Alignment of NMR spectra – Part IV: Advanced Alignment Alignment of NMR spectra – Part V: Reaction Monitoring (I)
nmrlearner News from NMR blogs 0 02-10-2011 08:29 PM
[NMR analysis blog] Alignment of NMR spectra – Part V: Reaction Monitoring (I)
Alignment of NMR spectra – Part V: Reaction Monitoring (I) Previous posts on this series: 1. Alignment of NMR spectra – Part I: The problem 2. Alignment of NMR spectra – Part II: Binning / Bucketing 3. Alignment of NMR spectra – Part III: Global Alignment 4. Alignment of NMR spectra – Part IV: Advanced Alignment Following the progression of chemical reactions by NMR is becoming more and more popular. Quoting Michael A. Bernstein et al. (Magn. Reson. Chem. 2007; 45: 564–571)
nmrlearner News from NMR blogs 0 02-08-2011 08:16 PM
[NMR analysis blog] Alignment of NMR spectra – Part IV: Advanced Alignment
Alignment of NMR spectra – Part IV: Advanced Alignment Previous posts on this series: Alignment of NMR spectra – Part I: The problem Alignment of NMR spectra – Part II: Binning / Bucketing Alignment of NMR spectra – Part III: Global Alignment As I mentioned in my previous post, simple alignment based on shifting or referencing the whole spectrum is not enough in cases where there are different local chemical shift fluctuations. Resorting back to the synthetic data set used in the previous posts, let me introduce a semi-automatic method designed specifically to align spectra having...
nmrlearner News from NMR blogs 0 02-07-2011 07:53 PM
[NMR analysis blog] Alignment of NMR spectra – Part III: Global Alignment
Alignment of NMR spectra – Part III: Global Alignment Previous posts on this series: Alignment of NMR spectra – Part I: The problem Alignment of NMR spectra – Part II: Binning / Bucketing We have seen that binning helps in minimizing, for example, the effect of pH-induced fluctuations in chemical shift so that, in the field of NMR-based metabonomics studies, ensuring that signals for a given metabolite appear at the same location in all spectra. One evident disadvantage of binning is that it greatly reduces the spectral resolution (e.g. in a 500 MHz instrument, a typical 64 Kb...
nmrlearner News from NMR blogs 0 02-03-2011 06:51 PM
[NMR analysis blog] Alignment of NMR spectra – Part II: Binning / Bucketing
Alignment of NMR spectra – Part II: Binning / Bucketing In my last post, I wrote that spectra of biological samples are usually poorly aligned due to wide changes in chemical shift arising from small variations in pH or other sample conditions such as ionic strength or temperature. The most widely used method of addressing this chemical shift variability across spectra is by means of the so-called binning (or bucketing), procedure that consists in segmenting a spectrum into small areas (bins / buckets) and taking the area under the spectrum for each segment. Preferably, the size of the...
nmrlearner News from NMR blogs 0 01-31-2011 06:03 AM
[NMR analysis blog] Alignment of NMR spectra – The problem: Part I
Alignment of NMR spectra – The problem: Part I The chemical shift is of great importance for NMR spectroscopy because it reflects the chemical environment of the nuclides under observation providing detailed information about the structure of a molecule. Although the chemical shift of a nucleus in a molecule is generally assumed to be fairly stable, there are a number of experimental factors (pH, ionic strength, solvent, field inhomogeneity –bad shimming, temperature, etc) which might produce slight or even quite significant variations in chemical shifts. This is particularly important...
nmrlearner News from NMR blogs 0 01-28-2011 04:52 AM
[NMR paper] Partial alignment of biomolecules: an aid to NMR characterization.
Partial alignment of biomolecules: an aid to NMR characterization. Related Articles Partial alignment of biomolecules: an aid to NMR characterization. Curr Opin Chem Biol. 2001 Oct;5(5):584-90 Authors: Prestegard JH, Kishore AI Partial alignment of biomolecules in solution has added a new dimension to structural investigation by high-resolution NMR methods. Applications to proteins, nucleic acids and carbohydrates now abound. Limitations initially associated with compatibility of biomolecules with the liquid-crystal media commonly used to...
nmrlearner Journal club 0 11-19-2010 08:44 PM
alignment in a magnetic field
hi all, I have a general question about alignment in a magnetic field. For me, alignment in alignment media is easier to grasp because of interactions that I am familiar with as a chemist. But, whats the principle behind molecules that align in a magnetic field? There are a lot of examples like cyanometmyoglobin (from the Prestegard paper) where paramagnetic susceptibility plays a role. Thats understandable from my side. But what about for instance short DNA dimers (helices), collagen gels or bacteriophages? I could not really find a nice (clear to me) explanation, why these...
Hydrazin NMR Questions and Answers 1 09-23-2010 06:13 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



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 11:20 AM.


Map