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 06-29-2005, 04:53 AM
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

Completely Automated, Highly Error-Tolerant Macromolecular Structure Determination from Multidimensional Nuclear Overhauser Enhancement Spectra and Chemical Shift Assignments
Kuszewski, J.; Schwieters, C. D.; Garrett, D. S.; Byrd, R. A.; Tjandra, N.; Clore, G. M.;
J. Am. Chem. Soc. 2004; 126(20); 6258-6273


Abstract:

The major rate-limiting step in high-throughput NMR protein structure determination involves the calculation of a reliable initial fold, the elimination of incorrect nuclear Overhauser enhancement (NOE) assignments, and the resolution of NOE assignment ambiguities. We present a robust approach to automatically calculate structures with a backbone coordinate accuracy of 1.0-1.5 Å from datasets in which as much as 80% of the long-range NOE information (i.e., between residues separated by more than five positions in the sequence) is incorrect. The current algorithm differs from previously published methods in that it has been expressly designed to ensure that the results from successive cycles are not biased by the global fold of structures generated in preceding cycles. Consequently, the method is highly error tolerant and is not easily funnelled down an incorrect path in either three-dimensional structure or NOE assignment space. The algorithm incorporates three main features: a linear energy function representation of the NOE restraints to allow maximization of the number of simultaneously satisfied restraints during the course of simulated annealing; a method for handling the presence of multiple possible assignments for each NOE cross-peak which avoids local minima by treating each possible assignment as if it were an independent restraint; and a probabilistic method to permit both inactivation and reactivation of all NOE restraints on the fly during the course of simulated annealing. NOE restraints are never removed permanently, thereby significantly reducing the likelihood of becoming trapped in a false minimum of NOE assignment space. The effectiveness of the algorithm is demonstrated using completely automatically peak-picked experimental NOE data from two proteins: interleukin-4 (136 residues) and cyanovirin-N (101 residues). The limits of the method are explored using simulated data on the 56-residue B1 domain of Streptococcal protein G.
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] Auto assignment of N15 C13 EDIT noesy experments
Auto assignment of N15 C13 EDIT noesy experments Dear NMR wikiers could you please suggest any auto assignment web servers online to assign N-15 & C13- EDIT NOESY experiments data? Thanking you
nmrlearner News from other NMR forums 0 09-29-2011 07:27 AM
[NMR paper] Automated NMR structure calculation with CYANA.
Automated NMR structure calculation with CYANA. Related Articles Automated NMR structure calculation with CYANA. Methods Mol Biol. 2004;278:353-78 Authors: Güntert P This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Protein structure calculation from NMR data.
Protein structure calculation from NMR data. Related Articles Protein structure calculation from NMR data. Methods Mol Biol. 2002;173:267-83 Authors: Mal TK, Bagby S, Ikura M
nmrlearner Journal club 0 11-24-2010 08:49 PM
[Question from NMRWiki Q&A forum] How to keep XPLOR structure calculation from exploding?
How to keep XPLOR structure calculation from exploding? Trying to calculate a structure using sa.inp script and the energy in the cooling loop increases instead of going down. In the end there is a message ****&&&& rerun job with smaller timestep (i.e., 0.003)But making the timestep smaller does not help. Could anyone suggest where to look? edit: I've also commented out my restrains thinking that maybe my noe's are too whacky, but still structure diverges.
nmrlearner News from other NMR forums 0 11-02-2010 11:22 PM
Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm
Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm John J. Kuszewski, Robin Augustine Thottungal, G. Marius Clore and Charles D. Schwieters Journal of Biomolecular NMR; 2008; 41(4); pp 221-239 Abstract: We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258–6273). The improved protocol includes...
Abe Journal club 0 09-21-2008 11:43 PM
protein structure calculation
Hi! every one! I wanted to get in contact with people solving the structure of protein by using NMR. I am learning the process and i have many basics problem related with the work. cheers!
premprakash NMR Questions and Answers 0 03-29-2007 02:33 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 11:00 AM.


Map