Kavraki, Lydia E.2009-06-032009-06-032007Heath, Allison P.. "Towards multiscale protein simulations: Moving from coarse-grain to all-atom models." (2007) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/20511">https://hdl.handle.net/1911/20511</a>.https://hdl.handle.net/1911/20511Multiscale 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.71 p.application/pdfengCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.Computer scienceThesisTHESIS COMP.SCI. 2007 HEATH