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 02-03-2013, 10:13 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,416
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 Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

8 February 2012
Publication year: 2012
Source:Structure, Volume 20, Issue 2



The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent “blind” assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR.
Highlights

? Automated assignment and structure calculation from NMR NOESY spectra were assessed ? Routine, fully automated determination of protein structures is feasible ? Good stereochemical and geometric quality alone does not indicate structure accuracy





More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
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
[NMR paper] An integrated platform for automated analysis of protein NMR structures.
An integrated platform for automated analysis of protein NMR structures. Related Articles An integrated platform for automated analysis of protein NMR structures. Methods Enzymol. 2005;394:111-41 Authors: Huang YJ, Moseley HN, Baran MC, Arrowsmith C, Powers R, Tejero R, Szyperski T, Montelione GT Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Automated analysis of protein NMR assignments and structures.
Automated analysis of protein NMR assignments and structures. Related Articles Automated analysis of protein NMR assignments and structures. Chem Rev. 2004 Aug;104(8):3541-56 Authors: Baran MC, Huang YJ, Moseley HN, Montelione GT
nmrlearner Journal club 0 11-24-2010 10:01 PM
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...
nmrlearner Journal club 0 08-25-2010 02:04 PM
[NMR paper] An automated approach for clustering an ensemble of NMR-derived protein structures in
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Related Articles An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Eng. 1996 Nov;9(11):1063-5 Authors: Kelley LA, Gardner SP, Sutcliffe MJ
nmrlearner Journal club 0 08-22-2010 02:20 PM
[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
[Stan NMR blog] Is protein structure determination by NMR a routine?
Is protein structure determination by NMR a routine? An interview with Chris Spronk of 'Spronk NMR Consultancy' More...
nmrlearner News from NMR blogs 0 08-21-2010 05:42 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 - 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 12:15 PM.


Map