DescriptionThe purpose of this proposal is to renew our XRAC Allocation TG-MCB100109. During the past year, this allocation has provided us with sufficient resources to further optimize our weighted ensemble path sampling software for the efficient simulation of rare events and to apply the software to the simulation of association kinetics for a model protein-peptide system (the MDM2-p53 peptide complex). We now request a larger allocation to enable the application of the weighted ensemble approach to explicit solvent simulations of binding events for a model protein-protein complex (barnase-barstar complex) with rigorous calculation of association rates. This allocation will also enable the QM/MM simulations of a diffusion-controlled chemical reaction in solution (the addition of azide ion to a series of triphenylmethyl-derived cations) with the aid of the weighted ensemble approach. These applications will be important milestones two grand challenges in computational chemistry: 1) the simulation of protein binding events, and 2) the simulation of chemical reactions in solution. It would not be possible to make meaningful progress on these simulations without the requested allocation on the XSEDE resources.
OrganizationUniversity of Pittsburgh
Sponsor Campus GridOSG-XSEDE
Principal Investigator
Lillian Chong
Field Of ScienceMolecular and Structural Biosciences