Coarse-grained Brownian dynamics (BD) simulation for the substrate peptide- HIV protease system. Transition of the peptide substrate from an unbound to a final bound state is shown, and the protein flaps have to open to allow for the substrate binding. The total simulation length in this run was 2 microsecond.
Chang, C.E.A., Trylska J., Tozzini V. and McCammon J. A., Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations. Chemical Biology & Drug Design.2007,69:5-13
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Yeclanoide 3 years ago