NMR paper Ab initio NMR chemical-shift calculations based on the combined fragmentation method.

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[NMR paper] Ab initio NMR chemical-shift calculations based on the combined fragmentation method.

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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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04-16-2013, 07:46 PM

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Ab initio NMR chemical-shift calculations based on the combined fragmentation method.

Ab initio NMR chemical-shift calculations based on the combined fragmentation method.

Related Articles Ab initio NMR chemical-shift calculations based on the combined fragmentation method.

Phys Chem Chem Phys. 2013 Apr 12;

Authors: Tan HJ, Bettens RP

Abstract
NMR chemical shift is a molecular property that can be computed from first principles. In this work we show that by utilizing our combined fragmentation method (CFM), one is able to accurately compute this property for small proteins. Without nonbonded interactions, the root mean square errors (RMSEs) compared to the full calculations for (1)H, (13)C, (15)N, (17)O and (33)S were 0.340, 0.649, 3.052, 6.928 and 0.122 ppm respectively, while with the inclusion of nonbonded interactions the RMSEs for (1)H, (13)C, (15)N, (17)O and (33)S were 0.038, 0.253, 0.681, 3.480 and 0.052 ppm respectively.

PMID: 23584332 [PubMed - as supplied by publisher]

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