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NMR processing:
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Ab initio:
GeNMR
Cyana
XPLOR-NIH
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Fragment-based:
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Template-based:
GeNMR
I-TASSER
Refinement:
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Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
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Secondary structure from chemical shifts:
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MICS caps, β-turns
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Flexibility from chemical shifts:
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Interactions from chemical shifts:
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Chemical shifts re-referencing:
Shiftcor
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SAVES2 or SAVES4
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B-factor
Molecular dynamics:
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From structure:
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Sparta+
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ArShift- Aromatic
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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:
camLILA
ccSOL
Camfold
camGroEL
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Isotope labeling:
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Solid-state NMR:
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Default A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.

A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.

A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase.

Bioorg Med Chem. 2018 Feb 22;:

Authors: Nagatoishi S, Yamaguchi S, Katoh E, Kajita K, Yokotagawa T, Kanai S, Furuya T, Tsumoto K

Abstract
19F NMR has recently emerged as an efficient, sensitive tool for analyzing protein binding to small molecules, and surface plasmon resonance (SPR) is also a popular tool for this purpose. Herein a combination of 19F NMR and SPR was used to find novel binders to the ATP-binding pocket of MAP kinase extracellular regulated kinase 2 (ERK2) by fragment screening with an original fluorinated-fragment library. The 19F NMR screening yielded a high primary hit rate of binders to the ERK2 ATP-binding pocket compared with the rate for the SPR screening. Hit compounds were evaluated and categorized according to their ability to bind to different binding sites in the ATP-binding pocket. The binding manner was characterized by using isothermal titration calorimetry and docking simulation. Combining 19F NMR with other biophysical methods allows the identification of multiple types of hit compounds, thereby increasing opportunities for drug design using preferred fragments.


PMID: 29510947 [PubMed - as supplied by publisher]



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