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

Current approaches for the fitting and refinement of atomic models into cryo-EM maps usingCCP-EM

“…CCP-EM (Wood et al , 2015) contains various tools to facilitate model fitting/refinement, including DockEM (Roseman, 2000), Choyce (Rawi et al , 2010) and Flex-EM (Joseph et al , 2016) for fitting and morphing of the structure at low resolution in cases where only information about the overall shape of the molecule is available, and REFMAC 5 (Murshudov et al , 2011) for full atomic model refinement at higher resolutions where at least some bulky side chains are visible. It should be noted that other software tools are available for the fitting and refinement of atomic models into cryo-EM maps, including DireX (Schröder et al , 2007), MDFF (Trabuco et al , 2008), Cryo-Fit (Kirmizialtin et al , 2015), Rosetta (Wang et al , 2016) and phenix.real_space_refine (Afonine et al , 2018). …”

Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application

“…In crystallography, software packages such as Phenix.refine (Afonine et al, 2012), ARP/wARP (Lamzin et al, 2012) and GlobalPhasing PipeDream (Sharff et al, 2011) are designed to link and automate (in different ways and to a different extent, depending on the package) a structure solution stage, structure refinement step(s) and automated ligand fitting. While these packages are still mostly designed for use with x-ray diffraction data, modifications have been implemented to allow working with EM maps (for example CCPEM (Wood et al, 2015) (Burnley et al, 2017), Phenix CryoFit (Kirmizialtin et al, 2015) or Rosetta (Wang et al, 2016b)). Next steps should be linking these EM-specific variations into a single pipeline, which would ideally require minimal user input, and output a final model ready to be used for further drug design.…”

Molecular simulations of the ribosome and associated translation factors

“…Further, MD simulations biased by cryo-EM density maps have been successfully used as a tool for high-resolution structure determination (see Ref. 7 and references therein). Finally, and possibly most importantly, MD simulations have enabled us to move from mere correlations to an understanding of causes and effects.…”