Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions.

By Serdal Kirmizialtin, J. Loerke, E. Behrmann, C. Spahn, K. Sanbonmatsu. 2015

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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “(iv) CryoFit uses molecular dynamics to perform flexible fitting of a model to a cryo-EM map (Kirmizialtin et al., 2015; Kim et al., 2019).”
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, background): “Two notable recent extensions of this concept are Flex-EM (Joseph et al., 2016) and CryoFIT (Kirmizialtin et al., 2015), which each use more complex energy functions based upon cross-correlation between experimental and simulated density maps to reduce the tendency for trapping in local minima.”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “It should be noted that other software tools are available for the ﬁtting and reﬁne-ment of atomic models into cryo-EM maps, including DireX (Schro¨der et al. , 2007), MDFF (Trabuco et al. , 2008), Cryo-Fit (Kirmizialtin et al. , 2015), Rosetta (Wang et al. , 2016) and phenix.real_space_reﬁne (Afoni”