NMR paper Structural analysis of non-native states of proteins by NMR methods.

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[NMR paper] Structural analysis of non-native states of proteins by NMR methods.

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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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08-22-2010, 02:27 PM

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Structural analysis of non-native states of proteins by NMR methods.

Structural analysis of non-native states of proteins by NMR methods.

Related Articles Structural analysis of non-native states of proteins by NMR methods.

Curr Opin Struct Biol. 1996 Feb;6(1):24-30

Authors: Shortle DR

Established NMR methods are increasingly being applied to the non-native states of proteins. For small denatured proteins, full assignment of proton, 15N and 13C resonances is often straightforward. Sensitive methods exist for detecting fractionally populated alpha helices and beta strands, but defining transient interactions among side chains is proving more problematic. The non-native states of several small proteins are being intensively investigated to address a number of questions about protein folding.

PMID: 8696969 [PubMed - indexed for MEDLINE]

Source: PubMed

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