Abstract
BackgroundDramatic progress has recently been made in cryo-electron microscopy technologies, which now make possible the reconstruction of a growing number of biomolecular structures to near-atomic resolution. However, the need persists for fitting and refinement approaches that address those cases that require modeling assistance.MethodsIn this paper, we describe algorithms to optimize the performance of such medium-resolution refinement methods. These algorithms aim to automatically optimize the parameters that define the density shape of the flexibly fitted model, as well as the time-dependent damper cutoff distance. Atomic distance constraints can be prescribed for cases where extra containment of parts of the structure is helpful, such as in regions where the density map is poorly defined. Also, we propose a simple stopping criterion that estimates the probable onset of overfitting during the simulation.ResultsThe new set of algorithms produce more accurate fitting and refinement results, and yield a faster rate of convergence of the trajectory toward the fitted conformation. The latter is also more reliable due to the overfitting warning provided to the user.ConclusionsThe algorithms described here were implemented in the new Damped-Dynamics Flexible Fitting simulation tool “DDforge” in the Situs package.
Highlights
Dramatic progress has recently been made in cryo-electron microscopy technologies, which make possible the reconstruction of a growing number of biomolecular structures to near-atomic resolution
Side-chain optimization was used in all cases except thermosome, since in this case the focus was on modeling the considerable large-scale deformations between the atomic model and the EM map
Validation test: lactoferrin To demonstrate the level of accuracy achievable by means of the new features described in the previous section, we consider the simulated case of lactoferrin
Summary
Dramatic progress has recently been made in cryo-electron microscopy technologies, which make possible the reconstruction of a growing number of biomolecular structures to near-atomic resolution. Over the last few years, experimental techniques for cryoelectron microscopy (cryo-EM) have evolved dramatically, making it possible for some structures to be solved at near-atomic resolution During a typical cryo-EM workflow, resolution normally increases over time, from a rather low value, as the quality and quantity of the images improves. These considerations indicate that there is still a need to be able to obtain atomic models from cryo-EM maps having medium resolutions, in the range of 5–10 Å. Several new flexiblefitting approaches have been published since which can be broadly grouped into a few types:
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