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

		BioNMR > Educational resources > Journal club
Computational approaches to the interpretation of NMR data for studying protein dynamics

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

02-03-2013, 10:13 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,174

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

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...

Did you find this post helpful?

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

« Previous Thread | Next 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