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Towards multiscale protein simulations: Moving from coarse-grain to all-atom models
Heath, Allison P.
Kavraki, Lydia E.
Master of Arts
Multiscale methods are becoming increasingly promising as a way to characterize the dynamics of large protein systems on biologically relevant time-scales. The underlying assumption of these methods is that is possible to move reliably between different resolutions. This thesis presents a method that efficiently generates realistic all-atom protein structures starting from the C, atom positions, as obtained for instance from extensive coarse-grain simulations. The method, a Reconstruction Algorithm for COarse Grain Structures (RACOGS), is validated by reconstructing ensembles of coarse grain structures obtained during folding simulations of the proteins src-SH3 and S6. The results show that RACOGS consistently produces low energy, all-atom structures. A comparison of the free energy landscapes calculated using the coarse-grain structures versus the all-atom structures shows good correspondence and little distortion in the protein folding landscape. These results demonstrate that RACOGS can be used as a tool in multiscale modeling to reliably move from coarse-grain structures to all-atom structures.