2019Kim CryoFit
Citation
Kim, D.N., Moriarty, N.W., Kirmizialtin, S., Afonine, P.V., Poon, B., Sobolev, O.V., Adams, P.D. and Sanbonmatsu, K. 2019. Cryo_fit: Democratization of flexible fitting for cryo-EM. Journal of structural biology. 208, 1 (2019), 1–6.
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 threedimensional (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.
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Links
https://www.sciencedirect.com/science/article/pii/S1047847719301285