NMR paper RFAC, a program for automated NMR R-factor estimation.

		BioNMR > Educational resources > Journal club
[NMR paper] RFAC, a program for automated NMR R-factor estimation.

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

11-18-2010, 09:15 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

RFAC, a program for automated NMR R-factor estimation.

RFAC, a program for automated NMR R-factor estimation.

Related Articles RFAC, a program for automated NMR R-factor estimation.

J Biomol NMR. 2000 Jun;17(2):137-51

Authors: Gronwald W, Kirchhöfer R, Görler A, Kremer W, Ganslmeier B, Neidig KP, Kalbitzer HR

A computer program (RFAC) has been developed, which allows the automated estimation of residual indices (R-factors) for protein NMR structures and gives a reliable measure for the quality of the structures. The R-factor calculation is based on the comparison of experimental and simulated 1H NOESY NMR spectra. The approach comprises an automatic peak picking and a Bayesian analysis of the data, followed by an automated structure based assignment of the NOESY spectra and the calculation of the R-factor. The major difference to previously published R-factor definitions is that we take the non-assigned experimental peaks into account as well. The number and the intensities of the non-assigned signals are an important measure for the quality of an NMR structure. It turns out that for different problems optimally adapted R-factors should be used which are defined in the paper. The program allows to compute a global R-factor, different R-factors for the intra residual NOEs, the inter residual NOEs, sequential NOEs, medium range NOEs and long range NOEs. Furthermore, R-factors can be calculated for various user defined parts of the molecule or it is possible to obtain a residue-by-residue R-factor. Another possibility is to sort the R-factors according to their corresponding distances. The summary of all these different R-factors should allow the user to judge the structure in detail. The new program has been successfully tested on two medium sized proteins, the cold shock protein (TmCsp) from Termotoga maritima and the histidine containing protein (HPr) from Staphylococcus carnosus. A comparison with a previously published R-factor definition shows that our approach is more sensitive to errors in the calculated structure.

PMID: 10921778 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMRpipe Yahoo group] Re: Signal-to-noise estimation Re: Signal-to-noise estimation Greetings, Dear Pipers, and Happy Winter Holidays, or Whatever ... There are lots of ways this could be done, depending on how rigorous you want to be, how More...	NMRpipe Yahoo group news	News from other NMR forums	0	12-25-2011 10:35 PM
[NMRpipe Yahoo group] Signal-to-noise estimation Signal-to-noise estimation Hello! I am new in "NMR world". I have some basic questions regarding the NMRPipe. I would like to know if there is a manner to estimate the signal-to-noise More...	NMRpipe Yahoo group news	News from other NMR forums	0	12-25-2011 10:35 PM
Numerical estimation of relaxation and diffusion distributions in two dimensions Numerical estimation of relaxation and diffusion distributions in two dimensions Publication year: 2011 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 21 July 2011</br> J., Mitchell , T.C., Chandrasekera , L.F., Gladden</br> Graphical abstract Graphical abstract:Highlights:?We review two-dimensional inversion methods for NMR data. ? Methods reviewed are applicable to relaxation time or diffusion data. ? Solutions to Fredholm integral equations of the first kind are presented. ? Selection of optimum smoothing for...	nmrlearner	Journal club	0	07-27-2011 11:32 PM
Backbone resonance assignment and order tensor estimation using residual dipolar couplings Backbone resonance assignment and order tensor estimation using residual dipolar couplings Abstract An NMR investigation of proteins with known X-ray structures is of interest in a number of endeavors. Performing these studies through nuclear magnetic resonance (NMR) requires the costly step of resonance assignment. The prevalent assignment strategy does not make use of existing structural information and requires uniform isotope labeling. Here we present a rapid and cost-effective method of assigning NMR data to an existing structureâ??either an X-ray or computationally modeled...	nmrlearner	Journal club	0	06-15-2011 02:31 AM
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
[NMR paper] NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor receptor complex. Visualization of human TGF-alpha binding determinants through nuclear Overhauser enhancement analysis. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles NMR study of the transforming growth factor-alpha (TGF-alpha)-epidermal growth factor receptor complex. Visualization of human TGF-alpha binding determinants through nuclear Overhauser enhancement analysis. J Biol...	nmrlearner	Journal club	0	08-22-2010 02:20 PM
[NMR paper] Estimation of the intracellular free ADP concentration by 19F NMR studies of fluorine Estimation of the intracellular free ADP concentration by 19F NMR studies of fluorine-labeled yeast phosphoglycerate kinase in vivo. Related Articles Estimation of the intracellular free ADP concentration by 19F NMR studies of fluorine-labeled yeast phosphoglycerate kinase in vivo. Biochemistry. 1993 May 11;32(18):4895-902 Authors: Williams SP, Fulton AM, Brindle KM Yeast phosphoglycerate kinase was selectively fluorine-labeled in vivo by inducing enzyme synthesis in stationary phase cells in the presence of 5-fluorotryptophan. Inducible...	nmrlearner	Journal club	0	08-21-2010 11:53 PM
MONTE: a program for automated NMR assignment MONTE: An automated Monte Carlo based approach to nuclear magnetic resonance assignment of proteins. Hitchens TK, Lukin JA, Zhan Y, McCallum SA, Rule GS. Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA. J Biomol NMR. 2003 Jan;25(1):1-9. http://www.bionmr.com/forum/style_images/monte.gif Monte website	nmrlearner	NMR software	0	07-17-2005 03:04 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