Fitting to a Cryo-EM Map using MD Simulation



Cryo_fit fits biomolecule (protein and nucleic acids) to cryo-EM map that is reconstructed by single particle analysis using molecular dynamics simulation


With many crystallography groups shifting to cryogenic electron microscopy (cryo-EM), there is a high demand for software that can produce atomistic models for high resolution cryo-EM datasets. Therefore, we are incorporating our automated cryo-EM density fitting method (cryo_fit) into a widely used software suite for macromolecular structure determination (PHENIX). Cryo_fit produces all-atom models highly consistent with the EM density and is being used to construct models for many functional complexes (including one of the first all-atom models of the human ribosome, revealing a new conformational change specific to eukaryotic ribosomes: subunit rolling). Two key advantages of the cryo_fit are its speed and the preservation of stereochemistry information. Its fast speed allows cryo-EM scientists to run on a single laptop (several hours for a ribosome modeling without the need for GPU) instead of thousands of cores. It uses a reduced model molecular dynamics potential that allows us to preserve stereochemistry information. As an additional advantage, secondary and tertiary contact potentials can be specified to place additional restraints on contacts within a cutoff keeping them intact during the fitting process.

How to Fit Cryo EM Maps




How Cryo_fit Works


How to Run Cryo_fit

See the tutorial notes for cryo_fit


See the cryo_fit FAQ


S. Kirmizialtin, J. Loerke, E. Behrmann, C. MT. Spahn, K. Y Sanbonmatsu, Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions, Methods Enzymol., 558, 2015, 497-514