These projects involve the SARS-CoV-2 receptor binding domain (RBD) and its target receptor in humans, ACE2. We are simulating these proteins alone and in complex with each other (and with and without glycosylation). We will build Markov State Models using the Fah simulation data, which will help us identify the metastable states of each protein/protein complex. Given these experiments, we hope to be able to explain the impact of glycosylation on RBD conformational dynamics as well as identify whether there are shifts in metastable states upon RBD:ACE2 binding. Ultimately, the knowledge gained here will help infom drug design efforts.
Note: 17313-6 replace 17307-9, as 17307-9 used a different, less stable integrator.
List of Contributors
This project is managed by Ivy Zhang at Memorial Sloan Kettering Cancer Center.
Ivy Zhang is a Tri-Institutional Computational Biology and Medicine graduate student in the Chodera lab at the Memorial Sloan Kettering Cancer Center.
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