NMR paper Calculating protein structures from NMR data.

		BioNMR > Educational resources > Journal club
[NMR paper] Calculating protein structures 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

08-22-2010, 03:31 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

Calculating protein structures from NMR data.

Calculating protein structures from NMR data.

Related Articles Calculating protein structures from NMR data.

Methods Mol Biol. 1997;60:157-94

Authors: GÃ¼ntert P

PMID: 9276248 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Open Biochem J. 2010;4:83-95 Authors: Sikic K, Tomic S, Carugo O Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...	nmrlearner	Journal club	0	02-05-2011 05:28 PM
[NMR paper] 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	nmrlearner	Journal club	0	11-25-2010 08:21 PM
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] Calculating protein structures from NMR data. Calculating protein structures from NMR data. Related Articles Calculating protein structures from NMR data. Methods Mol Biol. 1997;60:157-94 Authors: GÃ¼ntert P	nmrlearner	Journal club	0	08-22-2010 03:03 PM
[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
[NMR paper] Computational methods for determining protein structures from NMR data. Computational methods for determining protein structures from NMR data. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Computational methods for determining protein structures from NMR data. Biochem Pharmacol. 1990 Jul 1;40(1):15-22 Authors: Gippert GP, Yip PF, Wright PE, Case DA The general procedures by which solution structures of proteins may be deduced from distance and angular constraints derived from NMR are reviewed, with an emphasis on practical aspects of...	nmrlearner	Journal club	0	08-21-2010 10:48 PM
[NMR paper] Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Related Articles Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Proteins. 1990;8(4):377-85 Authors: Kim Y, Prestegard JH Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling...	nmrlearner	Journal club	0	08-21-2010 10:48 PM
[NMR analysis blog] Basics on Arrayed-NMR Data Analysis (Part III): Extracting and calculating useful NMR Basics on Arrayed-NMR Data Analysis (Part III): Extracting and calculating useful NMR related molecular information After the basic introductory posts on arrayed NMR experiments, it’s now time to get some action and see how to extract relevant information from these experiments and calculate useful NMR related parameters such as diffusion, relaxation times, kinetics constants, etc. Actually, in this post I will cover the first case, that is, the analysis of PFG experiments to calculate diffusion coefficients. The reason for this is twofold: (1) I have a nice PFG data set whilst the...	nmrlearner	News from NMR blogs	0	08-21-2010 09:12 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