NMR paper Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain

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[NMR paper] Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain

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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, 03:31 PM

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Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain

Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.

Related Articles Automated resonance assignment of proteins using heteronuclear 3D NMR. 2. Side chain and sequence-specific assignment.

J Chem Inf Comput Sci. 1997 May-Jun;37(3):467-77

Authors: Li KB, Sanctuary BC

A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures the similarity between each detected spin pattern and 20 standard amino acid coupling patterns. Both chemical shift and topologically likeness are considered. The mapping algorithm uses the amino acid type information to direct detected polypeptides to proper position onto protein primary sequence. The assignment protocol can be applied to spin systems generated by many different approaches. We designed a few computer programs to derive a protein's backbone and side chain spin systems using heteronuclear 3D NMR. The results was then input to the sequential assignment protocol. All of the algorithms were tested on NMR data of a 90-residue N-domain of chicken skeletal troponin-C.

PMID: 9177001 [PubMed - indexed for MEDLINE]

Source: PubMed

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