Ali Saglam and Lillian Chong Presented Protein-protein Binding Pathway using Fully-continuous, Explicit-solvent Simulations

The latest study by Lillian Chong and Ali Saglam, a postdoc in the Faeder Lab, demonstrated the power of the weighted ensemble (WE) strategy in enabling explicit-solvent MD simulation of a protein–protein binding process.(Click here for the protein-protein binding simulation video) Their results provide a number of insights regarding the binding mechanism that cannot be obtained by laboratory experiments.

The research by Lillian Chong group appeared in the Royal Society of Chemistry journal Chemical Science (DOI: 10.1039/C8SC04811H). The WE strategy and others like it have great promise in providing insights involving binding kinetics for a variety of research areas, including biophysics, catalysis, protein engineering, and material design.

They pointed out that the simulation could now be completed within 10 days on a GPU using 16 NVIDIA Tesla P100 GPUs at a time, WE-enabled atomistic simulations of multi-ms protein binding processes are now practical on typical resources. The WE strategy have great potential in providing insights involving binding kinetics for a variety of research areas, including biophysics, catalysis, protein engineering, and material design.