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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 08-11-2008, 12:05 PM
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Default PhD positions in molecular simulation - Max Planck Institute, Germany

Hello. I found this PhD position on naturejobs.com

"""
PhD positions at the Max Planck Institute for Biophysical Chemistry, Gottingen, Germany.

PhD student positions in the computational biomolecular dynamics group at the Max Planck Institute for biophysical Chemistry in Gottingen, Germany are available to start immediately.
Possible projects include:

* the development and application of highly efficient enhanced sampling algorithms based on collective coordinates;
* the rational design of model membrane channels; the study of membrane-channel interactions;
* the development of accurate and efficient simulation techniques for the affinity prediction of putative blockers to membrane channels;
* the development and application of ensemble refinement techniques to study protein structure and dynamics based on NMR data.

All projects will use molecular dynamics and related computational techniques and will be carried out in close collaboration with experimental groups.

The successful candidate should have a degree in physics or chemistry, should have basic knowledge of structural biology and should have a strong interest in computational biophysics. Payment will be according to the German TVoD standard.

To learn more about other projects in the group, please visit: http://www.mpibpc.gwdg.de/groups/de_groot

The Max Planck Society seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply.
The Max Planck Society is committed to employing more handicapped individuals and especially encourages them to apply.

Please send your application documents before August 31th, 2008 as copies and not originals, as we cannot send documents back. Applications by email are preferred.
Applicants should send an application letter + CV (including the names of at least two people who would be willing to send a letter of recommendation) to: (preferably by email)

Dr. Bert de Groot
Computational biomolecular dynamics group
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Goettingen
Germany
email: bgroot@gwdg.de

"""
http://www.nature.com/naturejobs/science/jobs/64515
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