Cryo_fit: Democratization of flexible fitting for cryo-EM

Doo Nam Kim; Nigel W Moriarty; Serdal Kirmizialtin; Pavel V Afonine; Billy Poon; Oleg V Sobolev; Paul D Adams; Karissa Sanbonmatsu

doi:10.1016/j.jsb.2019.05.012

Cryo_fit: Democratization of flexible fitting for cryo-EM

J Struct Biol. 2019 Oct 1;208(1):1-6. doi: 10.1016/j.jsb.2019.05.012. Epub 2019 Jul 3.

Authors

Doo Nam Kim¹, Nigel W Moriarty², Serdal Kirmizialtin³, Pavel V Afonine², Billy Poon², Oleg V Sobolev², Paul D Adams⁴, Karissa Sanbonmatsu⁵

Affiliations

¹ Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
² Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, USA.
³ Chemistry Program, Science Division, New York University, Abu Dhabi, United Arab Emirates.
⁴ Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, USA; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
⁵ Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA; New Mexico Consortium, Los Alamos, NM, USA. Electronic address: kys@lanl.gov.

Abstract

Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. The package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential of cryo-EM.

Keywords: Correlation coefficient; Cryo-EM; Flexible fitting; Molecular dynamics; Phenix.

Cryo_fit: Democratization of flexible fitting for cryo-EM

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