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NMR processing:
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NMR assignment:
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MARS
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Side-chains:
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NOEs:
UNIO ATNOS-Candid
UNIO Candid
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Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
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UNIO ATNOS-Candid
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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
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Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
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Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
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NMR model quality:
NOEs, other restraints:
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RPF scores
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Chemical shifts:
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Vasco
iCing
RDCs:
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Anisofit
Pseudocontact shifts:
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Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
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STAN
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Verify_3D
Harmony
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NMR spectrum prediction:
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MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
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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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  • 1 Post By peter.lukavsky

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Default Postdocs, Students, Technician in RNA-protein NMR at CEITEC (Brno/CZ)

Dear colleagues, the Lukavsky Lab has openings for two postdocs, students and one technician at CEITEC (Brno/CZ) to work on RNA-based regulation of gene expression. We are focused on understanding molecular principles of RNA-protein assemblies regulating gene expression at the posttranscriptional level. In the cytoplasm, gene expression is timely and spatially coordinated to ensure that proteins are produced at the right place and time in the cell. Failure to properly transport and localize mRNAs and to control protein expression can lead to impairment of memory formation, neurobiological diseases and cancer.
We plan to study regulatory RNA elements found in neuronal mRNAs important for learning, memory formation and neurobiological diseases and their interaction with protein partners. We put a strong focus on alternative splicing, mRNA transport and translational control.
Our main structural tool is NMR spectroscopy, which we have successfully applied to determine several structures of large, regulatory RNAs and complexes. Our structural work is always accompanied by biochemical and functional studies to gain profound insights how regulatory RNAs and their complexes function in the cell.
CEITEC is a vibrant work place, with excellent colleagues and infrastructure for structural biology including six high-field NMR instruments from 500 to 950 MHz equipped with cryo-probes.

Successful candidates should be highly motivated and creative and share our fascination for RNA structure and function. Previous experience in molecular biology, biophysics and biochemistry are a plus. Good communication and interpersonal skills and fluency in spoken and written English are required.

For contact: peter.lukavsky@ceitec.muni.cz
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