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 03-06-2015, 12:45 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.

NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.

Related Articles NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.

J Biomol NMR. 2015 Mar 4;

Authors: Jang R, Wang Y, Xue Z, Zhang Y

Abstract
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14*? in Round 1 and 3.18 to 1.71*? in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.


PMID: 25737244 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment
NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment Abstract NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements....
nmrlearner Journal club 0 03-04-2015 08:56 AM
[NMR paper] Information-driven modeling of large macromolecular assemblies using NMR data.
Information-driven modeling of large macromolecular assemblies using NMR data. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Information-driven modeling of large macromolecular assemblies using NMR data. J Magn Reson. 2014 Apr;241:103-14 Authors: van Ingen H, Bonvin AM Abstract Availability of high-resolution atomic structures is one of the prerequisites for a mechanistic understanding of biomolecular function. This atomic...
nmrlearner Journal club 0 11-18-2014 01:56 PM
A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.
A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination. A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination. Chemphyschem. 2011 Apr 4;12(5):915-8 Authors: Huber M, Hiller S, Schanda P, Ernst M, Böckmann A, Verel R, Meier BH
nmrlearner Journal club 0 03-29-2011 07:04 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] De novo protein structure determination using sparse NMR data.
De novo protein structure determination using sparse NMR data. Related Articles De novo protein structure determination using sparse NMR data. J Biomol NMR. 2000 Dec;18(4):311-8 Authors: Bowers PM, Strauss CE, Baker D We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models...
nmrlearner Journal club 0 11-19-2010 08:29 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] Relaxation data in NMR structure determination: model calculations for the lysozyme-G
Relaxation data in NMR structure determination: model calculations for the lysozyme-Gd3+ complex. Related Articles Relaxation data in NMR structure determination: model calculations for the lysozyme-Gd3+ complex. Proteins. 1991;10(2):117-29 Authors: Sutcliffe MJ, Dobson CM The effect of including paramagnetic relaxation data as additional restraints in the determination of protein tertiary structures from NMR data has been explored by a systematic series of model calculations. The system used for testing the method was the 2.0 A resolution...
nmrlearner Journal club 0 08-21-2010 11:16 PM
NMRFAM Workshop: NMR data collection and analysis for biological structure determination
NMRFAM Workshop: NMR data collection and analysis for biological structure determination LINK The NMR facility is pleased to announce its first NMRFAM workshop to be held from noon June 6 through noon June 9, 2006 in the Biochemistry Addition at the University of Wisconsin-Madison. The detailed program for the workshop is now available. Purpose This workshop will offer a unique opportunity for participants to experience a combination of hands-on computational sessions, presentations, and discussions focusing on recently developed tools as well as emerging methods in NMR data...
nmrlearner Conferences 0 05-23-2006 09:31 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 05:25 PM.


Map