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 08-05-2008, 01:16 PM
Junior Member
 
Join Date: Aug 2008
Posts: 5
Points: 60, Level: 1
Points: 60, Level: 1 Points: 60, Level: 1 Points: 60, Level: 1
Level up: 20%, 40 Points needed
Level up: 20% Level up: 20% Level up: 20%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 60
Downloads: 0
Uploads: 0
Default 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 Güntert, 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 application to a large number of proteins, with each data set including many NMR spectra, chemical shifts, NOE assignments, and calculated structures. We have developed the new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, which is designed to reduce the tediousness of organizing and manipulating a large number of NMR data sets. In combination with CYANA, the program for automated NOE assignment and structure determination, we have established a robust and highly optimized strategy for comprehensive protein structure analysis. An application of KUJIRA in accordance with our new strategy was carried out by a non-expert in NMR structure analysis, demonstrating that the accurate assignment of the chemical shifts and a high-quality structure of a small protein can be completed in a few weeks. The high completeness of the chemical shift assignment and the NOE assignment achieved by the systematic analysis using KUJIRA and CYANA led, in practice, to increased reliability of the determined structure.
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] 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] 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] 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...
nmrlearner Journal club 0 11-19-2010 08:29 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
[NMR paper] A systematic comparison of three structure determination methods from NMR data: depen
A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data. Related Articles A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data. J Biomol NMR. 1992 Jul;2(4):373-88 Authors: Liu Y, Zhao D, Altman R, Jardetzky O We have systematically examined how the quality of NMR protein structures depends on (1) the number of NOE distance constraints, (2) their assumed precision, (3) the method of structure calculation...
nmrlearner Journal club 0 08-21-2010 11:41 PM
[NMR paper] Efficient analysis of protein 2D NMR spectra using the software package EASY.
Efficient analysis of protein 2D NMR spectra using the software package EASY. Related Articles Efficient analysis of protein 2D NMR spectra using the software package EASY. J Biomol NMR. 1991 Jul;1(2):111-30 Authors: Eccles C, Güntert P, Billeter M, Wüthrich K The program EASY supports the spectral analysis of biomacromolecular two-dimensional (2D) nuclear magnetic resonance (NMR) data. It provides a user-friendly, window-based environment in which to view spectra for interactive interpretation. In addition, it includes a number of automated...
nmrlearner Journal club 0 08-21-2010 11:16 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 - 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 02:48 PM.


Map