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NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Old 09-08-2008, 11:22 AM
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Default NMR Spectroscopy - Gregg Siegal

Gregg Siegal, for the Cyttron consortium, gives an introduction to NMR:

http://www.bfsc.leidenuniv.nl/downlo...sis_by_NMR.ppt

The presentation is very well-annotated, so be sure to adjust your view accordingly.

More of the Cyttron lectures can be found here:

http://www.bfsc.leidenuniv.nl/teaching.html

Quote:
Cyttron Lectures

There are many different technologies for imaging the cellular and molecular components of life. Each technology reveals essential features, and is indispensable for full understanding of fundamental living processes. However, each also has limits that constrain its specific application. For instance, X-ray crystallography reveals the atomic structure, but requires the sample to be crystalline; NMR reveals molecular structure and dynamics, but cannot handle large molecular complexes; AFM can measure forces on (living) surfaces, but does not allow views of the inside of the sample; electron microscopy reveals the molecular architecture of the cell in nm resolution, but requires the sample to be fixed or frozen; there are many modes in light microscopy that give molecular information on localization and intermolecular distances, but their resolution is limited. All these modes of imaging are complementary and their areas of application only partially overlap. Cyttron aims to integrate these modes of imaging in a single platform, which requires tuning and optimizing the various constituent technologies and creating a common visualization and modelling platform which allows easy correlation of multi-modal data.

In this lecture series we will discuss the theory, application and integration of the important technologies for studying the molecular and cellular structures of life. There are 14 lectures by specialists in the field, 3 workshops on current developments and a conference on the biological applications of Cyttron.
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Another lecture by Gregg Siegal - NMR and Structural Biology
Gregg Siegal (Leiden Institute of Chemistry) discusses the application of NMR to structural biology. http://metprot.lic.gorlaeus.net/siegal/teaching/struc_biol/NMR_and_Structural_Biology.ppt The website of the LIC's protein chemistry department can be found here: http://protchem.lic.gorlaeus.net/index.php?nav=home
Dermot Educational web pages 0 09-08-2008 11:46 AM



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