Dartmouth University NMR lectures

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Dartmouth University NMR lectures

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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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09-04-2008, 02:19 PM

Rex

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Dartmouth University NMR lectures

The following Dartmouth University NMR lectures can be downloaded from their website:

Introduction to Protein Structure and NMR
JIGSAW and NMR
Computational Protein Design
Residual Dipolar Couplings (RDCs) in NMR Structural Biology
Nuclear Vector Replacement for Automated NMR Resonance Assignments and 3D Structure Homology Detection
Protein Flexibility (1): FIRST and NMA Basics
Protein Flexibility (2): Loop Closure and Inverse Kinematics
Protein Flexibility (3): ROCK and FRODA
Protein Flexibility (4): Applications of NMA to Protein-Protein and Ligand-Protein Binding
SemiDefinite Programming and Distance Geometry with Orientation Constraints
Graph Cuts for Energy Minimization and Assignment Problem (1)
Graph Cuts for Energy Minimization Problems (2)
Protein Unfolding by Using Residual Dipolar Couplings
Structure-Based Protein-Ligand Binding
Analyzing Protein Structures by Using an Ensemble Representation
NMR Resonance Assignment Assisted by Mass Spectrometry
Automated NMR Resonance Assignment
Enzyme Redesign by SVM
Flexible Ligand-Protein Docking

Further information for each lecture can be found at:
http://www.cs.dartmouth.edu/~donaldc...current/Notes/

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