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- W3022798094 abstract "HIV-1 capsid proteins (CAs) assemble into a capsid that encloses the viral RNA. The binding between a pair of C-terminal domains (CTDs) constitutes a major interface in both the CA dimers and the large CA assemblies. Here, we attempt to use a general residue-level coarse-grained model to describe the interaction between two isolated CTDs in Monte Carlo simulations. With the standard parameters that depend only on the residue types, the model predicts a much weaker binding in comparison to the experiments. Detailed analysis reveals that some Lennard-Jones parameters are not compatible with the experimental CTD dimer structure, thus resulting in an unfavorable interaction energy. To improve the model for the CTD binding, we introduce ad hoc modifications to a small number of Lennard-Jones parameters for some specific pairs of residues at the binding interface. Through a series of extensive Monte Carlo simulations, we identify the optimal parameters for the CTD–CTD interactions. With the refined model parame..." @default.
- W3022798094 created "2020-05-13" @default.
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- W3022798094 date "2017-04-01" @default.
- W3022798094 modified "2023-09-23" @default.
- W3022798094 title "Parameter Optimization for Interaction between C-Terminal Domains of HIV-1 Capsid Protein" @default.
- W3022798094 hasPublicationYear "2017" @default.
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