Micar21 Ltd. provides broad range of consulting services, including but not limited to:
Receptor structure generation and refinement
Indeed for the application of all our drug drug discovery services a good initial protein structure is required and often, especially in a case of membrane proteins, such experimental data is not available. Thus, our extensive experience in the classical (cMD), accelerated Molecular dynamics (aMD), Metadynamics and other enhanced sampling methods is of great help. We perform all our simulations on Nvidia GPU systems. These approaches are now well recognized because they provide information about the binding modes of given set of lead compounds, consider possibility of multiple binding modes and can contribute to the correctly rescoring the ligands by their affinity when the ligands are with unknown binding properties. Moreover, these methods can capture both the protein and ligand dynamics in a millisecond time range and provide a useful knowledge about the structural properties of any receptor. It should also be noted that in many cases these data are difficult to obtain with most experimental techniques. Thus, these approaches provide a valuable tool for the best lead compounds selection.
An example of such a integrated new workflow have been recently developed in a scientific collaboration with Schrodinger Inc. The combination of docking, cMD, aMD and FEP+ was successfully applied to both drug design and toxicity studies. Scientific paper about this topic is already available.