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 07-25-2015, 01:54 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
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 Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics.

Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics.

Related Articles Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics.

J Struct Biol. 2015 Jul 20;

Authors: Vögeli B, Olsson S, Riek R, Güntert P

Abstract
The study of the spatial sampling of biomolecules is essential to understanding the structure-dynamics-function relationship. We have established a protocol for the determination of multiple-state ensembles based on exact measurements of the nuclear Overhauser effect (eNOE). The protocol is practical since it does not require any additional data, while all other NMR data sets must be supplemented by NOE restraints. The question arises as to how much structural and dynamics information is shared between the eNOEs and other NMR probes. We compile one of the largest and most diverse NMR data sets of a protein to date consisting of eNOEs, RDCs and J couplings for GB3. We show that the eNOEs improve the back-prediction of RDCs and J couplings, either upon use of more than one state, or in comparison to conventional NOEs. Our findings indicate that the eNOE data is self-consistent, consistent with other data, and that the structural representation with multiple states is warranted.


PMID: 26206511 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics
Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics Publication date: Available online 20 July 2015 Source:Journal of Structural Biology</br> Author(s): Beat Vögeli, Simon Olsson, Roland Riek, Peter Güntert</br> The study of the spatial sampling of biomolecules is essential to understanding the structure-dynamics-function relationship. We have established a protocol for the determination of multiple-state ensembles based on exact measurements of the nuclear Overhauser effect (eNOE). The...
nmrlearner Journal club 0 07-20-2015 09:54 PM
Decoding 'sweet codes' that determine protein fates - Phys.Org
Decoding 'sweet codes' that determine protein fates - Phys.Org <img alt="" height="1" width="1" /> Decoding 'sweet codes' that determine protein fates Phys.Org Many experimentalists and theorists have taken on the challenge to solve this problem. NMR spectroscopy is one of the most promising experimental approaches for conformational analyses of the sugar chains because of its ability to determine geometrical ... Read here
nmrlearner Online News 0 09-15-2014 07:13 PM
Decoding 'sweet codes' that determine protein fates - EurekAlert (press release)
Decoding 'sweet codes' that determine protein fates - EurekAlert (press release) <img alt="" height="1" width="1" /> Decoding 'sweet codes' that determine protein fates EurekAlert (press release) Many experimentalists and theorists have taken on the challenge to solve this problem. NMR spectroscopy is one of the most promising experimental approaches for conformational analyses of the sugar chains because of its ability to determine geometrical ... Read here
nmrlearner Online News 0 09-13-2014 11:35 AM
[NMR paper] Towards a true protein movie: A perspective on the potential impact of the ensemble-based structure determination using exact NOEs
Towards a true protein movie: A perspective on the potential impact of the ensemble-based structure determination using exact NOEs Publication date: April 2014 Source:Journal of Magnetic Resonance, Volume 241</br> Author(s): Beat Vögeli , Julien Orts , Dean Strotz , Celestine Chi , Martina Minges , Marielle Aulikki Wälti , Peter Güntert , Roland Riek</br> Confined by the Boltzmann distribution of the energies of the states, a multitude of structural states are inherent to biomolecules. For a detailed understanding of a protein’s function, its entire...
nmrlearner Journal club 0 03-22-2014 01:28 AM
[NMR images] Traditional NMR uses coils to
http://michaelgr.files.wordpress.com/2007/05/nmr-protein-001.jpg?w=450 http://michaelgr.com/2007/05/24/look-at-them-proteins-a-better-nuclear-magnetic-resonance-probe-and-a-look-at-computational-protein-research/ 20/12/2011 4:11:48 PM GMT Traditional NMR uses coils to More...
nmrlearner NMR pictures 0 01-12-2012 09:30 PM
Methyl groups as probes of supra-molecular structure, dynamics and function
Methyl groups as probes of supra-molecular structure, dynamics and function Abstract The development of new protein labeling strategies, along with optimized experiments that exploit the label, have significantly impacted on the types of biochemical problems that can now be addressed by solution NMR spectroscopy. Here we describe how methyl labeling of key residues in a highly deuterated protein background has facilitated studies of the structure, dynamics and interactions of supra-molecular particles. The methyl-labeling approach is briefly reviewed, followed by a summary of...
nmrlearner Journal club 0 01-09-2011 12:46 PM
[NMR paper] Nmr probes of molecular dynamics: overview and comparison with other techniques.
Nmr probes of molecular dynamics: overview and comparison with other techniques. Related Articles Nmr probes of molecular dynamics: overview and comparison with other techniques. Annu Rev Biophys Biomol Struct. 2001;30:129-55 Authors: Palmer AG NMR spin relaxation spectroscopy is a powerful approach for characterizing intramolecular and overall rotational motions in proteins. This review describes experimental methods for measuring laboratory frame spin relaxation rate constants by high-resolution solution-state NMR spectroscopy, together...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Completeness of NOEs in protein structure: a statistical analysis of NMR.
Completeness of NOEs in protein structure: a statistical analysis of NMR. Related Articles Completeness of NOEs in protein structure: a statistical analysis of NMR. J Biomol NMR. 1999 Jun;14(2):123-32 Authors: Doreleijers JF, Raves ML, Rullmann T, Kaptein R The completeness of experimentally observed NOE restraints of a set of 97 NMR protein structures deposited in the PDB has been assessed. Completeness is defined as the ratio of the number of experimentally observed NOEs and the number of 'expected NOEs'. A practical definition of 'expected...
nmrlearner Journal club 0 08-21-2010 04:03 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 02:40 PM.


Map