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Samuel Coulbourn Flores, Nucleic acids research, September 29 (2013)
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Determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. Case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. Combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. Most existing methods either model all atoms explicitly, resulting in often prohibitive cost, or use approximations that lose interesting structural and dynamical detail. In this work, I introduce Internal Coordinate Flexible Fitting, which uses full atomic forces and flexibility in limited regions of a model, capturing extensive conformational rearrangements at low cost. I use it to turn multiple low-resolution density maps, crystallographic structures and biochemical information into unified all-atoms trajectories of ribosomal translocation. Internal Coordinate Flexible Fitting is three orders of magnitude faster than the most comparable existing method.

In this paper, I show how to semiflexibly fit ribosomes to low-resolution Cryo-EM density maps. The model also includes biochemical and biophysical forces and constraints. A series of maps are fitted, showing a full trajectory of riboosmal translation wi

License: MMB input file

This contains the manuscript, fitted structures, trajectory, and movies for the flexible fitting of the ribosome to Fischer et al.'s density maps.


I include the manuscript, movies, trajectory, and fitted structures. The trajectory may be used for experimental validation.

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