NMR paper New perceptions of transcription factor properties from NMR.

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[NMR paper] New perceptions of transcription factor properties from NMR.

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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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11-17-2010, 11:06 PM

nmrlearner

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New perceptions of transcription factor properties from NMR.

New perceptions of transcription factor properties from NMR.

Related Articles New perceptions of transcription factor properties from NMR.

Biochem Cell Biol. 1998;76(2-3):368-78

Authors: Bagby S, Arrowsmith CH, Ikura M

The complementarity of NMR and X-ray crystallography for biomacromolecular studies has been particularly evident in analysis of transcription factor structures and interactions. While X-ray crystallography can be used to tackle relatively complicated structural problems including multicomponent (three and higher) complexes, NMR studies have provided new insights into the nature of protein-DNA and protein-protein interactions that would be difficult to obtain by other biophysical methods. We describe herein some of the novel and important information recently derived from NMR studies of transcription factors.

PMID: 9923706 [PubMed - indexed for MEDLINE]

Source: PubMed

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