Journal
JOURNAL OF STRUCTURAL BIOLOGY
Volume 208, Issue 1, Pages 1-6Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jsb.2019.05.012
Keywords
Cryo-EM; Molecular dynamics; Flexible fitting; Correlation coefficient; Phenix
Funding
- NIH [NIGMS R01-GM072686, NIGMS P01-GM063210]
- US Department of Energy [DE-AC02-05CH11231]
- NSF [MCB-1413700]
- NYU Abu Dhabi Faculty Research Fund [ST181]
- U.S. Department of Energy National Nuclear Security Administration [89233218CNA000001]
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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.
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