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 11-19-2010, 08:29 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,778
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 An approach for high-throughput structure determination of proteins by NMR spectrosco

An approach for high-throughput structure determination of proteins by NMR spectroscopy.

Related Articles An approach for high-throughput structure determination of proteins by NMR spectroscopy.

J Biomol NMR. 2000 Nov;18(3):229-38

Authors: Medek A, Olejniczak ET, Meadows RP, Fesik SW

An approach is described for rapidly determining protein structures by NMR that utilizes proteins containing 13C-methyl labeled Val, Leu, and Ile (delta1) and protonated Phe and Tyr in a deuterated background. Using this strategy, the key NOEs that define the hydrophobic core and overall fold of the protein are easily obtained. NMR data are acquired using cryogenic probe technology which markedly reduces the spectrometer time needed for data acquisition. The approach is demonstrated by determining the overall fold of the antiapoptotic protein, Bcl-xL, from data collected in only 4 days. Refinement of the Bcl-xL structure to a backbone rmsd of 0.95 A was accomplished with data collected in an additional 3 days. A distance analysis of 180 different proteins and structure calculations using simulated data suggests that our method will allow the global folds of a wide variety of proteins to be determined.

PMID: 11142513 [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
[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] An algebraic geometry approach to protein structure determination from NMR data.
An algebraic geometry approach to protein structure determination from NMR data. Related Articles An algebraic geometry approach to protein structure determination from NMR data. Proc IEEE Comput Syst Bioinform Conf. 2005;:235-46 Authors: Wang L, Mettu RR, Donald BR Our paper describes the first provably-efficient algorithm for determining protein structures de novo, solely from experimental data. We show how the global nature of a certain kind of NMR data provides quantifiable complexity-theoretic benefits, allowing us to classify our...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] NMR analysis of in vitro-synthesized proteins without purification: a high-throughput
NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach. Related Articles NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach. FEBS Lett. 2002 Jul 31;524(1-3):159-62 Authors: Guignard L, Ozawa K, Pursglove SE, Otting G, Dixon NE A cell-free protein expression system was established that provides protein samples of adequate concentration and purity for direct NMR analysis. The Escherichia coli peptidyl-prolyl cis-trans isomerase PpiB was expressed in this system...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Determination of conformational equilibrium of peptides in solution by NMR spectrosco
Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: application to the calibration of mean-field solvation models. Related Articles Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: application to the calibration of mean-field solvation models. Biopolymers. 2001;60(2):79-95 Authors: Groth M, Malicka J, Rodziewicz- Motowid?o S, Czaplewski C, Klaudel L, Wiczk W, Liwo A Peptides occur in...
nmrlearner Journal club 0 11-19-2010 08:32 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: WŁthrich 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
[NMR paper] An approach to global fold determination using limited NMR data from larger proteins
An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. J Biomol NMR. 1996 Oct;8(3):360-8 Authors: Smith BO, Ito Y, Raine A, Teichmann S, Ben-Tovim L, Nietlispach D, Broadhurst RW, Terada T, Kelly M, Oschkinat H, Shibata T, Yokoyama S, Laue ED A combination of calculation and experiment is used to demonstrate that the global fold of...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] A high-resolution 1H NMR approach for structure determination of membrane peptides an
A high-resolution 1H NMR approach for structure determination of membrane peptides and proteins in non-deuterated detergent: application to mastoparan X solubilized in n-octylglucoside. Related Articles A high-resolution 1H NMR approach for structure determination of membrane peptides and proteins in non-deuterated detergent: application to mastoparan X solubilized in n-octylglucoside. J Biomol NMR. 1995 Jun;5(4):345-52 Authors: Seigneuret M, Lévy D Application of 1H 2D NMR methods to solubilized membrane proteins and peptides has up to now...
nmrlearner Journal club 0 08-22-2010 03:41 AM
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies Naohiro Kobayashi, Junji Iwahara, Seizo Koshiba, Tadashi Tomizawa, Naoya Tochio, Peter GŁntert, Takanori Kigawa and Shigeyuki Yokoyama Journal of Biomolecular NMR; 2007; 39(1) pp 31 - 52 Abstract: The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput...
stewart Journal club 0 08-05-2008 01:16 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 - 2020, 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 08:23 PM.


Map