NMR guides from Prof. Stone lab

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NMR guides from Prof. Stone lab

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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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05-07-2005, 10:01 AM

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The following NMR guides are available from Prof. Stone website

Protein dynamics
Dynamics Guide: from relaxation to dynamics parameters

Protein structure calculation
Structure Calculation Guide using XPLOR

Hardware
Spectrometer Hardware : Descriptions, diagrams, and recommended configurations
Tuning the Probe

Software
The VNMR File System
Common VNMR Commands
Setting Up Files to Run a New Pulse Program

Spectrometer Operation
Temperature Regulation
Temperature Calibration
Locking and Shimming : including both manual and gradient shimming
Defining Radiofrequency(RF) Channels (Transmitters and Amplifiers)
Chemical Shift Referencing
Pulse Width Calibration
Setting Up and Running Heteronuclear Proton-Detected Experiments
Setting Up and Running Triple Resonance Experiments
Archiving Your Data

Specialized Topics
Shaped (Frequency Selective) Pulses
Shifted Laminar Pulses (Frequency shifted rectangular or shaped pulses)

Theory
Triple Resonance Experiments

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