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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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Unread 09-22-2007, 11:13 PM
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Default Post-doctoral Position in NMR and Structural Biology

Post-doctoral Position in NMR and Structural Biology

We are looking for a candidate to apply for a one-year post-doctoral position at University René Descartes, Paris, France. The project involves solution NMR and molecular modeling investigations of proteins and their complexes. The candidate must have a Ph.D. in physical chemistry or related field with experience in computational protein chemistry, structure-based drug design, protein modeling, and NMR spectroscopy. The candidate should be able to tackle the state-of-the-art methodologies necessary for protein modeling and structure-based drug design studies. Please submit a copy of your application, including names and contact information of three references to serge.bouaziz@univ-paris5.fr

Vpr, the HIV-1 regulation protein, has been chemically synthesized in our laboratory and its structure solved by NMR (1). Vpr controls many events of the retroviral life cycle, nuclear import of the viral preintegration complex, replication in nondividing cells, arrest of the cell cycle in the G2 phase, stimulation of the viral transcription and regulation of the apoptosis in infected cells. These various activities of Vpr are made possible by interaction with cellular proteins among which several contain a WxxF motif within their sequence. This is the case of ANT the adenine nucleotide translocator, a mitochondrial protein. Moreover, short peptides containing a WxxF motif (2) or a WW (diW) motif (3) are able to interfere with Vpr, suppress the growth arrest phenotype mediated by Vpr and alleviate Vpr-mediated apoptosis.

The project consists in the study of the complex formed between the full protein Vpr and an ANT domain of 30 amino acids, containing the WxxF motif. Functional and structural results will make possible a new strategy in the design of antiviral molecules interfering with HIV-1 replication.

1. Morellet N. et al., 2003, J Mol Biol. 327(1):215-27
2. BouHamdan, M., et al., 1998, J Biol Chem. 273(14):8009-16
3. Yao, X.J., et al., 2002. J Biol Chem. 277(50):48816-26

Contact:
Serge Bouaziz
Phone: 33 (0) 1 53 73 95 78
Fax: 33 (0) 1 43 26 69 18
E-mail: serge.bouaziz@univ-paris5.fr

Universite Rene Descartes
Inserm U640 - CNRS UMR 8151
PARIS , France

Lab website: http://www.enscp.fr/labos/umr8151/index.htm
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