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 Rating: Thread Rating: 1 votes, 5.00 average. Display Modes
  #1  
Unread 08-25-2010, 02:04 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 Fully automated high-quality NMR structure determination of small (2)H-enriched prote

Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.

Related Articles Fully automated high-quality NMR structure determination of small (2)H-enriched proteins.

J Struct Funct Genomics. 2010 Aug 24;

Authors: Tang Y, Schneider WM, Shen Y, Raman S, Inouye M, Baker D, Roth MJ, Montelione GT


Determination of high-quality small protein structures by nuclear magnetic resonance (NMR) methods generally requires acquisition and analysis of an extensive set of structural constraints. The process generally demands extensive backbone and sidechain resonance assignments, and weeks or even months of data collection and interpretation. Here we demonstrate rapid and high-quality protein NMR structure generation using CS-Rosetta with a perdeuterated protein sample made at a significantly reduced cost using new bacterial culture condensation methods. Our strategy provides the basis for a high-throughput approach for routine, rapid, high-quality structure determination of small proteins. As an example, we demonstrate the determination of a high-quality 3D structure of a small 8 kDa protein, E. coli cold shock protein A (CspA), using
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Advances in automated NMR protein structure determination.
Advances in automated NMR protein structure determination. Advances in automated NMR protein structure determination. Q Rev Biophys. 2011 Mar 17;:1-53 Authors: Guerry P, Herrmann T Around half of all protein structures solved nowadays using solution-state nuclear magnetic resonance (NMR) spectroscopy have been because of automated data analysis. The pervasiveness of computational approaches in general hides, however, a more nuanced view in which the full variety and richness of the field appears. This review is structured around a comparison of...
nmrlearner Journal club 0 03-18-2011 06:00 PM
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks.
Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks. Towards fully automated structure-based NMR resonance assignment of (15)n-labeled proteins from automatically picked peaks. J Comput Biol. 2011 Mar;18(3):347-63 Authors: Jang R, Gao X, Li M Abstract In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow...
nmrlearner Journal club 0 03-10-2011 03:51 PM
[Optimization of the methods for small peptide solution structure determination by NMR spectroscopy].
. . Mol Biol (Mosk). 2010 Nov-Dec;44(6):1075-85 Authors: NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints from NMR spectra. At the same time, short charged peptides play an important role in a number of biological processes, in particular in pathogenesis of neurodegenerative...
nmrlearner Journal club 0 02-05-2011 05:28 PM
[NMR paper] Some NMR experiments and a structure determination employing a [15N,2H] enriched prot
Some NMR experiments and a structure determination employing a enriched protein. Related Articles Some NMR experiments and a structure determination employing a enriched protein. J Biomol NMR. 1998 Aug;12(2):259-76 Authors: Mal TK, Matthews SJ, Kovacs H, Campbell ID, Boyd J We present the results of studies of an aqueous sample of a highly enriched protein, the SH3 domain from Fyn. Measurements of 1H relaxation and interactions between H2O solvent and exchangeable protons are given, as well as a method for increasing the effective...
nmrlearner Journal club 0 11-17-2010 11:15 PM
Automated protein NMR structure determination in solution.
Automated protein NMR structure determination in solution. Automated protein NMR structure determination in solution. Methods Mol Biol. 2010;673:95-127 Authors: Gronwald W, Kalbitzer HR The main drawback of protein NMR spectroscopy today is still the extensive amount of time required for solving a single structure. The main bottleneck in this respect is the manual evaluation of the experimental spectra. A clear solution to this challenge is the development of automated methods for this purpose. At the current stage of development, this goal has...
nmrlearner Journal club 0 09-14-2010 02:03 PM
[NMR paper] Three-dimensional solution structure of the oxidized high potential iron-sulfur prote
Three-dimensional solution structure of the oxidized high potential iron-sulfur protein from Chromatium vinosum through NMR. Comparative analysis with the solution structure of the reduced species. Related Articles Three-dimensional solution structure of the oxidized high potential iron-sulfur protein from Chromatium vinosum through NMR. Comparative analysis with the solution structure of the reduced species. Biochemistry. 1995 Aug 8;34(31):9851-8 Authors: Bertini I, Dikiy A, Kastrau DH, Luchinat C, Sompornpisut P The NMR solution structure of...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[Ryan's blog] Is There Hope for Fully Automated Structure Elucidation?- New Article Published
Source: Ryan's blog Is There Hope for Fully Automated Structure Elucidation?- New Article Published Computer Assisted Structure Elucidation (CASE) is a major challenge in and of itself. We've been working on this for many, many years and we continue to make huge strides in this area. The technology is sound, the software is being...
nmrlearner News from NMR blogs 0 08-21-2010 08:57 PM
Fully Automated Protein NMR Structure Determination - ATNOS, MATCH, ASCAN and CANDID - Dr. Torsten Herrmann
Dr. Torsten Herrmann (for NMRFAM - the National Magnetic Resonance Facility at Madison) gives a presentation on the various techniques available for fully-automated protein NMR structure determination. It's available from here: http://www.nmrfam.wisc.edu/workshops/2006/Presentations/herrmann.pdf
Bertie Educational web pages 0 09-01-2008 02:03 AM


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 02:13 PM.


Map