Molecular Dynamics (MD) simulations are becoming an increasingly important computational tool in drug-discovery. In contrast to a static description of protein-ligand interactions, MD simulations contain explicit treatment of water and receptor motion, thus capturing the dynamic nature of protein-ligand interactions. These advantages make MD a powerful tool for investigating atomic-level interactions and fluctuations, which are at the heart of ligand binding affinity and selectivity.  Simulation Interactions Diagram (SID) is a new post-MD analysis tool for exploring the dynamics of protein-ligand interactions. We apply SID to gain insights into several important drug targets studied with stand-alone MD and with FEP simulations.  We present the results extracted from such analyses and show how these results may be can be used to to rationalize structure-activity relationship data and facilitate idea generation for prospective compounds.

Exploring MD simulations of protein-ligand complexes with SID

248th National Meeting (2014)

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