NMR paper Validity of using the radius of gyration as a restraint in NMR protein structure dete

		BioNMR > Educational resources > Journal club
[NMR paper] Validity of using the radius of gyration as a restraint in NMR protein structure dete

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

11-19-2010, 08:32 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

Validity of using the radius of gyration as a restraint in NMR protein structure dete

Validity of using the radius of gyration as a restraint in NMR protein structure determination.

Related Articles Validity of using the radius of gyration as a restraint in NMR protein structure determination.

J Am Chem Soc. 2001 Apr 25;123(16):3834-5

Authors: Huang X, Powers R

PMID: 11457122 [PubMed]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures. Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures. Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures. Proteins. 2011 Jan 6; Authors: Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal...	nmrlearner	Journal club	0	03-03-2011 12:34 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 paper] NMR structure note--solution structure of a bacterial BolA-like protein XC975 from a NMR structure note--solution structure of a bacterial BolA-like protein XC975 from a plant pathogen Xanthomonas campestris pv. campestris. Related Articles NMR structure note--solution structure of a bacterial BolA-like protein XC975 from a plant pathogen Xanthomonas campestris pv. campestris. J Biomol NMR. 2005 Feb;31(2):167-72 Authors: Chin KH, Lin FY, Hu YC, Sze KH, Lyu PC, Chou SH	nmrlearner	Journal club	0	11-24-2010 11:14 PM
Molecular basis of photochromism of a fluorescent protein revealed by direct 13C dete Molecular basis of photochromism of a fluorescent protein revealed by direct 13C detection under laser illumination Abstract Dronpa is a green fluorescent protein homologue with a photochromic property. A green laser illumination reversibly converts Dronpa from a green-emissive bright state to a non-emissive dark state, and ultraviolet illumination converts it to the bright state. We have employed solution NMR to understand the underlying molecular mechanism of the photochromism. The detail characterization of Dronpa is hindered as it is metastable in the dark state and spontaneously...	nmrlearner	Journal club	0	11-07-2010 02:47 PM
[Question from NMRWiki Q&A forum] How to convert Xplor distance restraint to Amber? How to convert Xplor distance restraint to Amber? HiI am wondering if anyone knows a way to convert Xplor distance_restraint files to Amber format (7 or 8 column).RegardsRaman Check if somebody has answered this question on NMRWiki QA forum	nmrlearner	News from other NMR forums	0	09-25-2010 07:47 AM
[NMR paper] Simulated annealing with restrained molecular dynamics using a flexible restraint pot Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints. ...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] NMR restraint analysis of transforming growth factor alpha: a key component for NMR s NMR restraint analysis of transforming growth factor alpha: a key component for NMR structure refinement. Related Articles NMR restraint analysis of transforming growth factor alpha: a key component for NMR structure refinement. Proteins. 1992 Aug;13(4):306-26 Authors: Brown FK, Hempel JC, Jeffs PW Structures of the protein, transforming growth factor alpha (TGF-alpha), have been derived from NMR data using distance geometry and subsequent energy refinement. Analysis of the sequential NOE distance bounds using a template algorithm provides a...	nmrlearner	Journal club	0	08-21-2010 11:45 PM
RDC refinement, via gyration tensor Hi, I am trying to find an alignment tensor for my RNA molecule. This I want to do by calculating the gyration tensor, and derive the alignment tensor. like in J. Biomol. NMR (2006) 35, pp. 103-115 problem is to do relatively simple manipulations in xplor For example calculate the product of x-coordinate times y-coordinates of all atoms in the PDB file.	Ramon989	NMR structure calculation	0	08-27-2007 12:39 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