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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
JournalJournal of Structural Biology
DOIs
StateAccepted/In press - Jan 1 2019

Fingerprint

Cryoelectron Microscopy
Molecular Dynamics Simulation
Software
Professional Competence
Computer Simulation
Growth

Keywords

  • Correlation coefficient
  • Cryo-EM
  • Flexible fitting
  • Molecular dynamics
  • Phenix

ASJC Scopus subject areas

  • Structural Biology

Cite this

Kim, D. N., Moriarty, N. W., Kirmizialtin, S., Afonine, P. V., Poon, B., Sobolev, O. V., ... Sanbonmatsu, K. (Accepted/In press). Cryo_fit: Democratization of flexible fitting for cryo-EM. Journal of Structural Biology. https://doi.org/10.1016/j.jsb.2019.05.012

Cryo_fit : Democratization of flexible fitting for cryo-EM. / Kim, Doo Nam; Moriarty, Nigel W.; Kirmizialtin, Serdal; Afonine, Pavel V.; Poon, Billy; Sobolev, Oleg V.; Adams, Paul D.; Sanbonmatsu, Karissa.

In: Journal of Structural Biology, 01.01.2019.

Research output: Contribution to journalArticle

Kim, DN, Moriarty, NW, Kirmizialtin, S, Afonine, PV, Poon, B, Sobolev, OV, Adams, PD & Sanbonmatsu, K 2019, 'Cryo_fit: Democratization of flexible fitting for cryo-EM', Journal of Structural Biology. https://doi.org/10.1016/j.jsb.2019.05.012
Kim, Doo Nam ; Moriarty, Nigel W. ; Kirmizialtin, Serdal ; Afonine, Pavel V. ; Poon, Billy ; Sobolev, Oleg V. ; Adams, Paul D. ; Sanbonmatsu, Karissa. / Cryo_fit : Democratization of flexible fitting for cryo-EM. In: Journal of Structural Biology. 2019.
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