TY - JOUR TI - Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps AU - Singharoy, Abhishek AU - Teo, Ivan AU - McGreevy, Ryan AU - Stone, John E AU - Zhao, Jianhua AU - Schulten, Klaus A2 - Brunger, Axel T VL - 5 PY - 2016 DA - 2016/07/07 SP - e16105 C1 - eLife 2016;5:e16105 DO - 10.7554/eLife.16105 UR - https://doi.org/10.7554/eLife.16105 AB - Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a radius of convergence of ~25 Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services. KW - cryoelectron microscopy KW - high-resolution KW - cloud computing KW - hybrid methods KW - B-factors KW - flexible fitting JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -