From NMR Data to Protein Structure

		BioNMR > Educational resources > Conferences
From NMR Data to Protein Structure

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

Rating:

Display Modes

08-18-2010, 01:53 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

From NMR Data to Protein Structure

From NMR Data to Protein Structure

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Protein structure calculation with data imputation: the use of substitute restraints Protein structure calculation with data imputation: the use of substitute restraints Abstract The amount of experimental restraints e.g., NOEs is often too small for calculating high quality three-dimensional structures by restrained molecular dynamics. Considering this as a typical missing value problem we propose here a model based data imputation technique that should lead to an improved estimation of the correct structure. The novel automated method implemented in AUREMOL makes a more efficient use of the experimental information to obtain NMR structures with higher accuracy. It...	nmrlearner	Journal club	0	01-09-2011 12:46 PM
[NMR paper] TOUCHSTONEX: protein structure prediction with sparse NMR data. TOUCHSTONEX: protein structure prediction with sparse NMR data. Related Articles TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins. 2003 Nov 1;53(2):290-306 Authors: Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J TOUCHSTONEX, a new method for folding proteins that uses a small number of long-range contact restraints derived from NMR experimental NOE (nuclear Overhauser enhancement) data, is described. The method employs a new lattice-based, reduced model of proteins that explicitly...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] Protein structure calculation from NMR data. Protein structure calculation from NMR data. Related Articles Protein structure calculation from NMR data. Methods Mol Biol. 2002;173:267-83 Authors: Mal TK, Bagby S, Ikura M	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] De novo protein structure determination using sparse NMR data. De novo protein structure determination using sparse NMR data. Related Articles De novo protein structure determination using sparse NMR data. J Biomol NMR. 2000 Dec;18(4):311-8 Authors: Bowers PM, Strauss CE, Baker D We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] Derivation of locally accurate spatial protein structure from NMR data. Derivation of locally accurate spatial protein structure from NMR data. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Derivation of locally accurate spatial protein structure from NMR data. Prog Biophys Mol Biol. 1993;59(3):285-339 Authors: Sherman SA, Johnson ME	nmrlearner	Journal club	0	08-21-2010 11:53 PM
[NMR paper] On deriving spatial protein structure from NMR or X-ray diffraction data. On deriving spatial protein structure from NMR or X-ray diffraction data. Related Articles On deriving spatial protein structure from NMR or X-ray diffraction data. Ciba Found Symp. 1991;161:150-9; discussion 159-66 Authors: van Gunsteren WF, Gros P, Torda AE, Berendsen HJ, van Schaik RC During the last decade it has become possible to derive the spatial structure of small proteins in solution using multidimensional NMR spectroscopy measurements and interpreting the data in terms of a chemical atomic model. The NMR experiments generate a set...	nmrlearner	Journal club	0	08-21-2010 11:16 PM
[NMR paper] Improved efficiency of protein structure calculations from NMR data using the program Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. Related Articles Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J Biomol NMR. 1991 Nov;1(4):447-56 Authors: GÃ¼ntert P, WÃ¼thrich K A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985) J. Mol. Biol., 186, 611) is described, which makes use of...	nmrlearner	Journal club	0	08-21-2010 11:12 PM
Structure-oriented methods for protein NMR data analysis Structure-oriented methods for protein NMR data analysis Publication year: 2010 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 3 March 2010</br> Guillermo A., Bermejo , Miguel, Llinás</br> More...	nmrlearner	Journal club	0	08-16-2010 03:50 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