Structural analysis  |   In silico structural studies and analyses
 
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NATIONAL CENTRE FOR SCIENTIFIC RESEARCH "DEMOKRITOS", NCSR-DEMOKRITOS
LOCATION:   Athens | http://www.demokritos.gr/
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In silico structural studies of globular proteins (homology 3D-modeling, molecular dynamics simulations and MD trajectory analyses) are undertaken, in the framework of scientific collaborations.

Person in charge: Dr. Metaxia Vlassi, Researcher A,  Please Contact here

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by
TYPE:   Computers for in silico structural studies of proteins (x2)
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LOCATION:   "Demokritos", Institute of Biosciences and Applications, Building 20
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HELLENIC PASTEUR INSTITUTE
LOCATION:   Athens, Greece | https://www.pasteur.gr/en/
RELEVANT STAFF:   Stathis Kotsakis , Vivi Miriagou
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In silico structural analyses can be performed at the HPIs computing center through the services offered by the Laboratory of Bacteriology.

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Available methods and programs are: Molecular Dynamics (Free Energy Perturbation and Umbrella Sampling) through the GROMACS package, small molecule parameterization for the Amber family of force fields using quantum mechanical simulations (Amber and ORCA packages), docking simulations using HADDOCK and AUTODOCK and model building through MODELLER.

AGRICULTURAL UNIVERSITY OF ATHENS
LOCATION:   Athens | https://www2.aua.gr/en
RELEVANT STAFF:   Elias Eliopoulos , Kostas Bethanis
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Structural studies are enriched with computational calculations and molecular simulations. To this end, Molecular Docking, Molecular Dynamics simulations (AMBER 12), Drug Screening and Molecular Mechanics and Modeling are available. 3D vision2 wireless glasses (nVIDIA) compatible with the above computer programs are also available.

Visit the provider's website: http://inspired.aua.gr/instruct/

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HP Intel Xeon by HP
TYPE:   Bioinformatics Server
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LOCATION:   75 Iera Odos, Athens 118 55, Greece, Agricultural University of Athens, Hassiotes Build., 1st Floor, Biotechnology Dept., Genetics Lab
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Server consists of 24 units of 8-core Intel Xeon 2.8GHz workstations with 32GB internal memory each.


FUNDER:   INSPIRED-AUA GSRT
 
 
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Intel Core i5-3570 by Intel
TYPE:   Computer for in silico structural studies
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LOCATION:   75 Iera Odos, Athens 118 55, Greece, Agricultural University of Athens, Hassiotes Build., 1st Floor, Biotechnology Dept., Physics Lab
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Intel Core i5-3570 CPU @3.40GHz x4


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UNIVERSITY OF IOANNINA
LOCATION:   Ioannina, Greece | https://www.uoi.gr/en/
RELEVANT STAFF:   Efstratios Mylonas
SERVICE DETAILS:   Not available.
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by
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UNIVERSITY OF CRETE
LOCATION:   Heraklion, Crete | http://en.uoc.gr/
RELEVANT STAFF:   Kathrin Kefala , Eustratios Mylonas
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Various programms for structural studies are used for the analyses of X-ray diffraction data. Concerning X-ray crystallography analysis, the ccp4i programm suite, phenix, pymol and coot are used. For Molecular dynamics Amber programm suite is used, and for SAXS data analysis ATSAS programm suite.

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Biochemistry Lab by
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