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 11-24-2010, 08:49 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,697
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 Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignm

Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment.

Related Articles Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment.

Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8009-14

Authors: Szyperski T, Yeh DC, Sukumaran DK, Moseley HN, Montelione GT

A suite of reduced-dimensionality (13)C,(15)N,(1)H-triple-resonance NMR experiments is presented for rapid and complete protein resonance assignment. Even when using short measurement times, these experiments allow one to retain the high spectral resolution required for efficient automated analysis. "Sampling limited" and "sensitivity limited" data collection regimes are defined, respectively, depending on whether the sampling of the indirect dimensions or the sensitivity of a multidimensional NMR experiments per se determines the minimally required measurement time. We show that reduced-dimensionality NMR spectroscopy is a powerful approach to avoid the "sampling limited regime"--i.e., a standard set of ten experiments proposed here allows one to effectively adapt minimal measurement times to sensitivity requirements. This is of particular interest in view of the greatly increased sensitivity of NMR spectrometers equipped with cryogenic probes. As a step toward fully automated analysis, the program AUTOASSIGN has been extended to provide sequential backbone and (13)C(beta) resonance assignments from these reduced-dimensionality NMR data.

PMID: 12060747 [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
Reduced dimensionality 3D HNCANfor unambiguous HN, CA and N assignment in proteins
Reduced dimensionality 3D HNCANfor unambiguous HN, CA and N assignment in proteins Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 8 February 2012</br> Manoj Kumar*Rout, Pushpa*Mishra, Hanudatta S.*Atreya, Ramakrishna V.*Hosur</br> We present here an improvisation of HNN (Panchal, Bhavesh et al. 2001)called RD 3D HNCANfor backbone (HN, CA andN) assignment inboth folded and unfolded proteins. This is a reduced dimensionality experiment which employsCAchemical shifts to improve dispersion. Distinct positive and negative peak patternsof various triplet...
nmrlearner Journal club 0 02-10-2012 09:13 AM
Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH
Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH Abstract We present reduced dimensionality (RD) 3D HN(CA)NH for efficient sequential assignment in proteins. The experiment correlates the 15N and 1H chemical shift of a residue (â??iâ??) with those of its immediate N-terminal (i â?? 1) and C-terminal (i + 1) neighbors and provides four-dimensional chemical shift correlations rapidly with high resolution. An assignment strategy is presented which combines the correlations observed in this experiment with amino acid type information obtained from 3D ...
nmrlearner Journal club 0 01-09-2012 08:08 AM
Aliasing in reduced dimensionality NMR spectra: (3,2)D HNHA and (4,2)D HN(COCA)NH experiments as examples
Aliasing in reduced dimensionality NMR spectra: (3,2)D HNHA and (4,2)D HN(COCA)NH experiments as examples Abstract Reduced dimensionality NMR spectra usually require very large spectral widths in the shared dimension. In this paper we show that aliasing can be introduced in reduced dimensionality NMR spectra either to decrease the acquisition time or increase the resolution of the experiments without losing information. The gains of introducing aliasing are illustrated with two examples, the (3,2)D HNHA and the (4,2)D HN(COCA)NH experiments. In both cases a reduction of the spectral...
nmrlearner Journal club 0 01-09-2011 12:46 PM
[NMR paper] NMR data collection and analysis protocol for high-throughput protein structure determination.
NMR data collection and analysis protocol for high-throughput protein structure determination. Related Articles NMR data collection and analysis protocol for high-throughput protein structure determination. Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10487-92 Authors: Liu G, Shen Y, Atreya HS, Parish D, Shao Y, Sukumaran DK, Xiao R, Yee A, Lemak A, Bhattacharya A, Acton TA, Arrowsmith CH, Montelione GT, Szyperski T A standardized protocol enabling rapid NMR data collection for high-quality protein structure determination is presented that...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] High-throughput inference of protein-protein interfaces from unassigned NMR data.
High-throughput inference of protein-protein interfaces from unassigned NMR data. Related Articles High-throughput inference of protein-protein interfaces from unassigned NMR data. Bioinformatics. 2005 Jun;21 Suppl 1:i292-301 Authors: Mettu RR, Lilien RH, Donald BR SUMMARY: We cast the problem of identifying protein-protein interfaces, using only unassigned NMR spectra, into a geometric clustering problem. Identifying protein-protein interfaces is critical to understanding inter- and intra-cellular communication, and NMR allows the study of...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] High-throughput 3D structural homology detection via NMR resonance assignment.
High-throughput 3D structural homology detection via NMR resonance assignment. Related Articles High-throughput 3D structural homology detection via NMR resonance assignment. Proc IEEE Comput Syst Bioinform Conf. 2004;:278-89 Authors: Langmead CJ, Donald BR One goal of the structural genomics initiative is the identification of new protein folds. Sequence-based structural homology prediction methods are an important means for prioritizing unknown proteins for structure determination. However, an important challenge remains: two highly...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] An efficient high-throughput resonance assignment procedure for structural genomics a
An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR. Related Articles An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR. Biochemistry. 2001 Dec 11;40(49):14727-35 Authors: Bhavesh NS, Panchal SC, Hosur RV Sequence specific resonance assignment is the primary requirement for all investigations of proteins by NMR methods. In the present postgenomic era where structural genomics and protein folding have...
nmrlearner Journal club 0 11-19-2010 08:44 PM
NMR in a crystallography-based high-throughput protein structure-determination enviro
NMR in a crystallography-based high-throughput protein structure-determination environment. Related Articles NMR in a crystallography-based high-throughput protein structure-determination environment. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1365-6 Authors: Wüthrich K An introduction is provided to three papers which compare corresponding protein crystal and NMR solution structures determined by the Joint Center for Structural Genomics (JCSG). Special mention is made of the JCSG strategy for combined use of the two...
nmrlearner Journal club 0 10-16-2010 03:56 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 06:16 PM.


Map