NMR paper Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone

		BioNMR > Educational resources > Journal club
[NMR paper] Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-25-2010, 08:21 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,697

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

Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone

Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions.

Related Articles Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions.

Angew Chem Int Ed Engl. 2005 May 30;44(22):3394-9

Authors: Lange OF, Grubmüller H, de Groot BL

PMID: 15912573 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...	nmrlearner	Journal club	0	02-11-2012 10:31 AM
Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations Nicolas L. Fawzi, Aaron H. Phillips, Jory Z. Ruscio, Michaeleen Doucleff, David E. Wemmer and Teresa Head-Gordon Journal of the American Chemical Society DOI: 10.1021/ja204315n http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/bEQEah_ik60	nmrlearner	Journal club	0	07-09-2011 07:11 AM
[NMR paper] Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation. Related Articles Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation. Eur Biophys J. 2002 Dec;31(7):504-20 Authors: Antes I, Thiel W, van Gunsteren WF Photoactive yellow protein (PYP) is a...	nmrlearner	Journal club	0	11-24-2010 08:58 PM
[NMR paper] Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations and multifield NMR relaxation data. Related Articles Helix motion in protein C12A-p8(MTCP1): comparison of molecular dynamics simulations and multifield NMR relaxation data. J Comput Chem. 2002 Dec;23(16):1577-86 Authors: Barthe P, Roumestand C, Déméné H, Chiche L The human p8(MTCP1) protein is constituted by an original disulfide bridged alpha-hairpin motif, and a third hydrophilic helix that appeared mobile and independent in NMR analysis. To get atomic...	nmrlearner	Journal club	0	11-24-2010 08:58 PM
[NMR paper] Simulated and NMR-derived backbone dynamics of a protein with significant flexibility Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain. Related Articles Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain. J Am Chem Soc. 2001 Apr 4;123(13):3021-36 Authors: Pfeiffer S, Fushman D, Cowburn D A 7.6 ns molecular dynamics trajectory of the betaARK1 PH domain in explicit water with appropriate ions was calculated at 300 K. Spectral densities...	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[NMR paper] Comparison of protein backbone entropy and beta-sheet stability: NMR-derived dynamics Comparison of protein backbone entropy and beta-sheet stability: NMR-derived dynamics of protein G B1 domain mutants. Related Articles Comparison of protein backbone entropy and beta-sheet stability: NMR-derived dynamics of protein G B1 domain mutants. J Am Chem Soc. 2001 Jan 10;123(1):185-6 Authors: Stone MJ, Gupta S, Snyder N, Regan L	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[NMR paper] The solution conformations of amino acids from molecular dynamics simulations of Gly- The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters. Related Articles The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters. Biochem Cell Biol. 1998;76(2-3):164-70 Authors: van der Spoel D The conformations that amino acids can adopt in the random coil state are of fundamental interest in the context of protein folding research and studies of protein-peptide interactions. To date, no...	nmrlearner	Journal club	0	11-17-2010 11:06 PM
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins. Related Articles Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins. Structure. 2010 Aug 11;18(8):923-933 Authors: Robustelli P, Kohlhoff K, Cavalli A, Vendruscolo M We introduce a procedure to determine the structures of proteins by incorporating NMR chemical shifts as structural restraints in molecular dynamics simulations. In this approach, the chemical shifts are expressed as differentiable...	nmrlearner	Journal club	0	08-17-2010 03:36 AM

« 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