NMR paper Assessing precision and accuracy of protein structures derived from NMR data.

		BioNMR > Educational resources > Journal club
[NMR paper] Assessing precision and accuracy of protein structures derived from NMR data.

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

Assessing precision and accuracy of protein structures derived from NMR data.

Assessing precision and accuracy of protein structures derived from NMR data.

Related Articles Assessing precision and accuracy of protein structures derived from NMR data.

Proteins. 2005 Jun 1;59(4):655-61

Authors: Snyder DA, Bhattacharya A, Huang YJ, Montelione GT

PMID: 15822105 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data. CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data. Related Articles CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data. BMC Struct Biol. 2010 Oct 29;10(1):39 Authors: Angyan AF, Szappanos B, Perczel A, Gaspari Z ABSTRACT: BACKGROUND: In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. These ensembles are usually substantially...	nmrlearner	Journal club	0	11-03-2010 10:44 AM
CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data - CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data - 7thSpace Interactive (press release) <img alt="" height="1" width="1" /> CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data 7thSpace Interactive (press release) These ensembles are usually substantially more diverse than conventional NMR ensembles and eliminate the expectation that a single conformer should fulfill ... Read here	nmrlearner	Online News	0	10-29-2010 09:32 PM
[NMR paper] Accuracy and precision of NMR relaxation experiments and MD simulations for character Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics. Proteins. 1997 Aug;28(4):481-93 Authors: Philippopoulos M, Mandel AM, Palmer AG, Lim C Model-free parameters obtained from nuclear magnetic resonance (NMR) relaxation...	nmrlearner	Journal club	0	08-22-2010 05:08 PM
[NMR paper] An assessment of the precision and accuracy of protein structures determined by NMR. An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors. J Mol Biol. 1994 Jun 24;239(5):601-7 Authors: Zhao D, Jardetzky O We tested the dependence of the accuracy and precision of calculated NMR structures on the errors of the distance constraints...	nmrlearner	Journal club	0	08-22-2010 03:33 AM
[NMR paper] An assessment of the precision and accuracy of protein structures determined by NMR. An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors. J Mol Biol. 1994 Jun 24;239(5):601-7 Authors: Zhao D, Jardetzky O We tested the dependence of the accuracy and precision of calculated NMR structures on the errors of the distance constraints...	nmrlearner	Journal club	0	08-22-2010 03:33 AM
[NMR paper] Conformational analysis of protein structures derived from NMR data. Conformational analysis of protein structures derived from NMR data. Related Articles Conformational analysis of protein structures derived from NMR data. Proteins. 1993 Nov;17(3):232-51 Authors: MacArthur MW, Thornton JM A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution...	nmrlearner	Journal club	0	08-22-2010 03:01 AM
Precision and Accuracy of NMR Structures - PSI Precision and Accuracy of NMR Structures - a presentation by the Protein Structure Initiative - is available to read from here: http://journals.iucr.org/services/nmr/precision.pdf More information about the PSI can be found here: http://www.structuralgenomics.org/	Rachel	Educational web pages	0	09-10-2008 05:32 PM
Assessing precision and accuracy of protein struct Editor's Corner Assessing precision and accuracy of protein structures derived from NMR data David A. Snyder 1 2, Aneerban Bhattacharya 1 2, Yuanpeng J. Huang 1 2, Gaetano T. Montelione 1 2 * 1Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854 2Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ 08854 *Correspondence to Gaetano T. Montelione, CABM-Rutgers University, 679 Hoes Lane, Piscataway, NJ...	nmrlearner	A test forum	0	05-07-2005 07:08 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