In-cell NMR [Commentary]

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In-cell NMR [Commentary]

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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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03-27-2012, 08:41 PM

nmrlearner

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In-cell NMR [Commentary]

In-cell NMR [Commentary]

Pielak, G. J., Tian, F....
Date: 2012-03-27

In PNAS, Renault et al. (1) describe an advance that will help reveal the atomic details of membrane proteins in living cells. Membrane proteins comprise one-third of all cellular proteins, including biologically crucial molecules such as ion channels, G protein-coupled receptors (GPCRs), and transporters. The GPCR superfamily alone comprises nearly half of our current drug targets. Despite their importance and prevalence, relatively few membrane protein structures are known. Of the more than 20,000 unique high-resolution protein structures in the Protein Data Bank (www.pdb.org) (2), less than 0.5% are membrane proteins. The paucity of membrane protein structures reflects difficulties in preparing... Read More

PNAS:
Number: 13
Volume: 109

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