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
In silico structural analyses can be performed at the HPIs computing center through the services offered by the Laboratory of Bacteriology.
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.
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/
Server consists of 24 units of 8-core Intel Xeon 2.8GHz workstations with 32GB internal memory each.
Intel Core i5-3570 CPU @3.40GHz x4
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.