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



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 08-14-2008, 10:15 PM
Junior Member
 
Join Date: Aug 2008
Posts: 6
Points: 72, Level: 1
Points: 72, Level: 1 Points: 72, Level: 1 Points: 72, Level: 1
Level up: 44%, 28 Points needed
Level up: 44% Level up: 44% Level up: 44%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 72
Downloads: 0
Uploads: 0
Default HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections

HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections
Gabriel Cornilescu, Arash Bahrami, Marco Tonelli, John L. Markley and Hamid R. Eghbalnia
Journal of Biomolecular NMR; 2007; 38(4); pp 341-351


Abstract:

We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, “High-resolution Iterative Frequency Identification of Couplings” (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C′ RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C′ vector represents a realistic “worst case analysis”. These couplings are among the smallest currently measured, and their determination in both isotropic and anisotropic media demands the highest measurement precision. The new approach yielded excellent quantitative agreement with values determined independently by the conventional 3D quantitative J NMR method (in cases where sample stability in oriented media permitted these measurements) but with a factor of 2–5 in time savings. The statistical measure of reliability, measuring the quality of each RDC value, offers valuable adjunct information even in cases where modest time savings may be realized.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[Question from NMRWiki Q&A forum] Method for indirect 13C-1H J-couplings measurements
Method for indirect 13C-1H J-couplings measurements Dear colleagues! 13C-1H J-couplings are essential in some areas of molecule structure research. I discovered modern methods implemented in our software and found the following: <ol> 13C J-resolved (recommended by Braun, Berger, Kalinovksy in 150 and more NMR experiments) J-HMBC (once I used it, but as I remember, it would't work with J
nmrlearner News from other NMR forums 0 11-12-2011 01:40 AM
Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins
Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins Abstract It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results. Here we present a suite of time- and sensitivity optimized NMR experiments for rapid measurement of up to six RDCs per residue. Including such an RDC data set, measured in less...
nmrlearner Journal club 0 09-17-2011 10:20 AM
[NMR paper] ALARM NMR: a rapid and robust experimental method to detect reactive false positives
ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens. Related Articles ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens. J Am Chem Soc. 2005 Jan 12;127(1):217-24 Authors: Huth JR, Mendoza R, Olejniczak ET, Johnson RW, Cothron DA, Liu Y, Lerner CG, Chen J, Hajduk PJ High-throughput screening (HTS) of large compound collections typically results in numerous small molecule hits that must be carefully evaluated to identify valid drug...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] SOS-NMR: a saturation transfer NMR-based method for determining the structures of pro
SOS-NMR: a saturation transfer NMR-based method for determining the structures of protein-ligand complexes. Related Articles SOS-NMR: a saturation transfer NMR-based method for determining the structures of protein-ligand complexes. J Am Chem Soc. 2004 Mar 3;126(8):2390-8 Authors: Hajduk PJ, Mack JC, Olejniczak ET, Park C, Dandliker PJ, Beutel BA An NMR-based alternative to traditional X-ray crystallography and NMR methods for structure-based drug design is described that enables the structure determination of ligands complexed to virtually...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] A general method for determining the electron self-exchange rates of blue copper prot
A general method for determining the electron self-exchange rates of blue copper proteins by longitudinal NMR relaxation. Related Articles A general method for determining the electron self-exchange rates of blue copper proteins by longitudinal NMR relaxation. J Am Chem Soc. 2002 Apr 17;124(15):4093-6 Authors: Jensen MR, Hansen DF, Led JJ A general NMR method is presented that allows a precise determination of the second-order rate constant, k(ese), for the electron self-exchange in blue copper proteins, from the longitudinal relaxation...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] A novel NMR method for determining the interfaces of large protein-protein complexes.
A novel NMR method for determining the interfaces of large protein-protein complexes. Related Articles A novel NMR method for determining the interfaces of large protein-protein complexes. Nat Struct Biol. 2000 Mar;7(3):220-3 Authors: Takahashi H, Nakanishi T, Kami K, Arata Y, Shimada I Identification of the interfaces of large (Mr > 50,000) protein-protein complexes in solution by high resolution NMR has typically been achieved using experiments involving chemical shift perturbation and/or hydrogen-deuterium exchange of the main chain amide...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] The chemical shift index: a fast and simple method for the assignment of protein seco
The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Related Articles The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry. 1992 Feb 18;31(6):1647-51 Authors: Wishart DS, Sykes BD, Richards FM Previous studies by Wishart et al. have demonstrated that 1H NMR chemical shifts are strongly dependent on the character and nature of protein secondary structure. In particular, it has been...
nmrlearner Journal club 0 08-21-2010 11:41 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 - 2017, 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 03:52 AM.


Map