Molecular Dynamics

Tools & Technologies - in silico Drug Discovery

Macromolecular targets such as proteins are complex systems and are often highly flexible in physiologically relevant environments. Protein folding and functional effects and protein-ligand interactions are significantly impacted by entropic contributions due to such mobility and solvation effects. Accurate prediction of such effects requires adequate sampling of system flexibility, which we address computationally through molecular dynamics (MD) simulations. In our experience, significant robustness can be added to virtual screening campaigns by incorporating protein binding site flexibility to enable ensemble docking approaches.

With our advanced GPU computing capabilities, Icagen has a strong track record of performing molecular dynamics for very large systems (> 200,000 atoms) in microsecond time scale. We have developed several tools for analyzing the MD trajectories and have experience in exploiting MD for virtual screening, protein stability studies, allosteric and transient binding site elucidation, free energy calculations, ligand engagement studies and binding thermodynamics and kinetics studies.