NMR paper Structure-based drug design: NMR-based approach for ligand-protein interactions.

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[NMR paper] Structure-based drug design: NMR-based approach for ligand-protein interactions.

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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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07-06-2014, 08:28 PM

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Structure-based drug design: NMR-based approach for ligand-protein interactions.

Structure-based drug design: NMR-based approach for ligand-protein interactions.

Related Articles Structure-based drug design: NMR-based approach for ligand-protein interactions.

Drug Discov Today Technol. 2006;3(3):241-5

Authors: Zhang X, Tang H, Ye C, Liu M

Abstract
The realization of the powerfulness in analyzing ligand-protein interactions at the atomic resolution has made NMR techniques increasingly attractive in drug discovery and development. With some significant new method developments during the past few years, NMR-based approaches will undoubtedly be helpful in high throughput screening and in providing structural and interaction information beneficial for new drug developments. Here in this review, instead of providing an exhaustive account of applications of NMR, we will seek to highlight some key points related to the solution state NMR methods for extracting information from both ligands and proteins.:

PMID: 24980524 [PubMed]

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