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: 20,399
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 Computational approaches to the interpretation of NMR data for studying protein dynamics

Computational approaches to the interpretation of NMR data for studying protein dynamics

2 March 2012
Publication year: 2012
Source:Chemical Physics, Volume 396



Experimental studies of protein structure and dynamics with NMR provide the classical example of the power of theoretical approaches for the interpretation of experimental results. In this paper we review recent developments in experimental techniques extending the applicability of NMR to the study of protein structure and motion, and advances in the theoretical description.
Graphical abstract

Highlights

? NMR data characterize protein motion on many timescales. ? Explicit motional models remain an important means to interpret NMR data remain important. ? Molecular dynamics simulations are increasingly valuable and ultimately more powerful. ? Extended or “accelerated” MD simulations can be directly compared with experimental data for longer timescales.





More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
The Dynamics of Dendrimers by NMR Relaxation: Interpretation Pitfalls
The Dynamics of Dendrimers by NMR Relaxation: Interpretation Pitfalls Luiz F. Pinto, Juan Correa, Manuel Martin-Pastor, Ricardo Riguera and Eduardo Fernandez-Megia http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja311908n/aop/images/medium/ja-2012-11908n_0008.gif Journal of the American Chemical Society DOI: 10.1021/ja311908n http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/jMsa8SYap7o
nmrlearner Journal club 0 01-23-2013 09:47 AM
Protein structure modeling using sparse NMR data [Biophysics and Computational Biology]
Protein structure modeling using sparse NMR data Thompson, J. M., Sgourakis, N. G., Liu, G., Rossi, P., Tang, Y., Mills, J. L., Szyperski, T., Montelione, G. T., Baker, D.... Date: 2012-06-19 While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that...
nmrlearner Journal club 0 06-20-2012 02:28 AM
[NMR paper] Thermodynamic interpretation of protein dynamics from NMR relaxation measurements.
Thermodynamic interpretation of protein dynamics from NMR relaxation measurements. Related Articles Thermodynamic interpretation of protein dynamics from NMR relaxation measurements. Protein Pept Lett. 2005 Apr;12(3):235-40 Authors: Spyracopoulos L Protein dynamics and thermodynamics can be characterized through measurements of relaxation rates of side chain (2)H and (13)C, and backbone (15)N nuclei using NMR spectroscopy. The rates reflect protein motions on timescales from picoseconds to milliseconds. Backbone and methyl side chain NMR...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] New approaches to the dynamic interpretation and prediction of NMR relaxation data fr
New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins. Related Articles New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins. Curr Opin Struct Biol. 2003 Apr;13(2):175-83 Authors: Brüschweiler R NMR relaxation experiments of isotopically labeled proteins provide a wealth of information on reorientational global and local dynamics on nanosecond and subnanosecond timescales for folded and nonfolded proteins in solution. Recent methodological advances in the...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic cal
Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR. Related Articles Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR. J Biomol NMR. 2002 Jun;23(2):139-50 Authors: Bernadó P, García de la Torre J, Pons M HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or C(alpha)-H vectors in a rigid protein structure starting from an atomic level representation. Thus...
nmrlearner Journal club 0 11-24-2010 08:49 PM
An introduction to NMR-based approaches for measuring protein dynamics.
An introduction to NMR-based approaches for measuring protein dynamics. An introduction to NMR-based approaches for measuring protein dynamics. Biochim Biophys Acta. 2010 Nov 5; Authors: Kleckner IR, Foster MP Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the...
nmrlearner Journal club 0 11-10-2010 02:29 PM
[NMR paper] Solid-state NMR approaches for studying membrane protein structure.
Solid-state NMR approaches for studying membrane protein structure. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--arjournals.annualreviews.org-images-AnnualReviews100x25.gif Related Articles Solid-state NMR approaches for studying membrane protein structure. Annu Rev Biophys Biomol Struct. 1992;21:25-47 Authors: Smith SO, Peersen OB
nmrlearner Journal club 0 08-21-2010 11:41 PM
[NMR paper] Computational methods for determining protein structures from NMR data.
Computational methods for determining protein structures from NMR data. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Computational methods for determining protein structures from NMR data. Biochem Pharmacol. 1990 Jul 1;40(1):15-22 Authors: Gippert GP, Yip PF, Wright PE, Case DA The general procedures by which solution structures of proteins may be deduced from distance and angular constraints derived from NMR are reviewed, with an emphasis on practical aspects of...
nmrlearner Journal club 0 08-21-2010 10:48 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 - 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 01:44 AM.


Map