Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and

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Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and

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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:

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08-16-2010, 03:50 AM

nmrlearner

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Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and

Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and fast pulsing methods for unfolded proteins

Publication year: 2010
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 12 June 2010

Dominique, Marion

Resonance assignment of intrinsically disordered proteins is made difficult by the extensive spectral overlaps. High-resolution 3D and 4D spectra are thus essential for this purpose. We have adapted the series of 3D BEST experiments proposed by Lescop et al [J. Magn. Reson. 187 (2007) 163–9] to the case of unfolded proteins. Longer acquisitions in the indirect dimensions are obtained by implementing semi-constant time evolution and sparse sampling. Using Maximum Entropy reconstruction for the indirect dimensions, the artifact intensity due to sparse sampling can be reduced to a level similar to the other sources of noise. The reduction of the sampled...

Source: Journal of Magnetic Resonance

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