Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography

Hybrid computational methods for combining structural data from different sources and resolutions are becoming an essential part of structural biology, especially as the field moves toward the study of large macromolecular assemblies. We have developed the molecular dynamics flexible fitting (MDFF) method for combining high-resolution atomic structures with cryo-electron microscopy (cryo-EM) maps, that results in atomic models representing the conformational state captured by cryo-EM. The method has been applied successfully to the ribosome, a ribonucleoprotein complex responsible for protein synthesis. MDFF involves a molecular dynamics simulation in which a guiding potential, based on the cryo-EM map, is added to the standard force field. Forces proportional to the gradient of the density map guide an atomic structure, available from X-ray crystallography, into high-density regions of a cryo-EM map. In this paper we describe the necessary steps to set up, run, and analyze MDFF simulations and the software packages that implement the corresponding functionalities.