Molecular Dynamics of proteins

 

The three-dimensional (3D) structure of biological macromolecules consists of a set of (x,y,z) coordinates for each atom of the molecule under investigation. The INSTRUCT ESFRI provides access to high specification, specialist equipment for the experimental determination of such coordinates. However, the 3D structure of any molecule is not completely rigid, but fluctuates over time due to the kinetic energy available at room temperature. Such flexibility is often directly relevant to the physiological function performed by proteins and nucleic acids in the cell. Although there are experiments that can provide information on the extent and time scales of macromolecular motions, computer simulation (Molecular Dynamics, MD) is the only technique that provides a full atomistic view of motions throughout all regions of the macromolecule.

The present demo highlights the use of the exploitation of Cloud technologies/solutions from the INDIGO PaaS to perform MD simulations using protocolized methods in VMs and the use of web interfaces to set up and analyze such simulations.