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NMR processing:
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NMR assignment:
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MARS
UNIO Match
PINE
Side-chains:
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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
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Chemical shifts:
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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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Unread 04-08-2011, 11:42 AM
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Default PhD position France

PhD position France

A PhD position is available at Rennes, France (collaboration between INRA-APBV (Yield under abiotic stress) and Cemagref (IRM-Food)). The project concerns in particular the update of the cellular and metabolic events which contribute to the reallocation of nitrogenous and carbon from senescing leaf tissues in order to define the mains determinants and to improve their efficiency. The ambition based on the two laboratories collaboration is to associate a fine analysis at the cellular level of the structural organization of leaf tissues by an original approach of NMR relaxometry with the concomitant description of the metabolic orientation of products stemming from organels and macromolecules degradation by metabolomic approaches. We will be also testing the validity of the NMR analysis as an efficient integrative tool to characterize senescing tissues and as an effective means of diagnostic and medium throughput phenotyping tool of stress conditions.

The project is highly interdisciplinary and will combine NMR for identification of water in different cell parts with cell biology techniques (non aqueous sub-cellular fractionnation, sub-cellular metabolic profiling, TEM, leaf senescence characterisation (molecular pysiological and biochemical markers).

Applications close - 15 Juin 2011.

Interested applicants should contact Dr Maja Musse (maja.musse@cemagref.fr) or Dr Laurent Leport (laurent.leport@univ-rennes1.fr) directly by submitting their CV.

Maja Musse, PhD
NMR/MRI group
Food process engineering research unit Cemagref
17, avenue de Cucillé
CS 64427
35044 Rennes cédex
tél : 02 23 48 21 79
fax : 02 23 48 21 15
mailto:maja.musse@cemagref.fr


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