Stan NMR blog Is protein structure determination by NMR a routine?

		BioNMR > NMR community > News from NMR blogs
[Stan NMR blog] Is protein structure determination by NMR a routine?

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

08-21-2010, 05:42 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

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...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[Question from NMRWiki Q&A forum] shake routine and ncon parameter shake routine and ncon parameter Trying to do molecular dynamics with explicit water molecules I came across a problem with SHAKE routine: shake reference = parameters bonds (hydrogen) (all) tolerance = 1.0e-06 nconstraints=8000end and error message after this is: X-PLOR>shake SHAKE> reference = parameters SHAKE> bonds (hydrogen) (all) SELRPN: 7142 atoms have been selected out of 11032 SELRPN: 11032 atoms have been selected out of 11032 SHKSET: reference = parameters %XREFIN-ERR: allocation for SHAKE-constraints exceeded ...	nmrlearner	News from other NMR forums	0	10-27-2011 11:42 PM
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction. Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction. Related Articles Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction. Structure. 2010 Dec 8;18(12):1678-1687 Authors: Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the...	nmrlearner	Journal club	0	12-08-2010 06:21 PM
[NMR software blog] Routine Prediction Routine Prediction Not everybody remembers how easy it is and how effective it can be to add (or correct) a few points at the beginning of the FID. Two years ago I explained how Linear Prediction works and how we can extrapolate the FID in both directions. This time I will show a simple practical application. I have observed that, in recent years, C-13 spectra acquired on Varian instruments require a much-larger-then-it-used-to-be phase correction. When I say correction, I mean first-order phase correction, because the zero-order correction is merely a different way of representing the...	nmrlearner	News from NMR blogs	0	12-01-2010 08:36 PM
[NMR paper] Structure determination of protein/RNA complexes by NMR. Structure determination of protein/RNA complexes by NMR. Related Articles Structure determination of protein/RNA complexes by NMR. Methods Enzymol. 2005;394:525-45 Authors: Wu H, Finger LD, Feigon J Structure determination of protein?RNA complexes in solution provides unique insights into factors that are involved in protein/RNA recognition. Here, we review the methodology used in our laboratory to overcome the challenges of protein?RNA structure determination by nuclear magnetic resonance (NMR). We use as two examples complexes recently...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
[NMR paper] Structure determination of protein complexes by NMR. Structure determination of protein complexes by NMR. Related Articles Structure determination of protein complexes by NMR. Methods Mol Biol. 2004;278:255-88 Authors: Nietlispach D, Mott HR, Stott KM, Nielsen PR, Thiru A, Laue ED This chapter describes nuclear magnetic resonance (NMR) methods that can be used to determine the structures of protein complexes. Many of these techniques are also applicable to other systems (e.g., protein-nucleic acid complexes). In the first section, we discuss methodologies for optimizing the sample conditions for...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] Determination of the NMR structure of the complex between U1A protein and its RNA pol Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element. Related Articles Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element. J Biomol NMR. 1998 Jan;11(1):59-84 Authors: Howe PW, Allain FH, Varani G, Neuhaus D RNA-protein recognition is critical to post-transcriptional regulation of gene expression, yet poorly understood at the molecular level. The relatively slow progress in understanding this important area of...	nmrlearner	Journal club	0	11-17-2010 11:06 PM
Lecture on protein structure determination by NMR Lecture on protein structure determination by NMR Dr. Robert Powers lecture material on NMR Spectroscopy and protein structure determination. More...	nmrlearner	Educational web pages	0	08-16-2010 03:50 AM
Structure Determination of Protein Complexes by NMR Structure Determination of Protein Complexes by NMR D. Nietlispach, H.R. Mott, K.M. Stott, P.R. Nielsen, A. Thiru & E.D. Laue The Department of Biochemistry, University of Cambridge Introduction As the structures of more proteins and domains are solved by structural genomics projects, the future of structural biology will be oriented more toward the study of macromolecular complexes. Since so many biological processes are mediated by interactions between proteins, it is important to study them at a molecular level. The study of protein-protein interactions also has applications in a...	timbo	Educational web pages	0	08-29-2008 02:43 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 Off Trackbacks are Off Pingbacks are Off Refbacks are Off