Cryo_fit: Democratization of flexible fitting for cryo-EM
نویسندگان
چکیده
منابع مشابه
PFfit: Hierarchical Flexible Fitting in 3D EM
We develop a hierarchical solution (PFfit) for fitting an atomic structure to a density map. We use scoring functions that account for steric clashes while maximizing the degree of fit between the protein and the density map, a non-uniform rotationally exhaustive Fourier-based search scheme, and a flexibility model that parametrizes shear and hinge bending motions available to each protein doma...
متن کاملRIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps
MOTIVATION To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component. RESULTS Here we p...
متن کاملAn Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map
Cryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic structures when the resolution of density maps is not sufficiently high. Geometrical shape representation of secondary structural components in a medium-resol...
متن کاملFitting low-resolution cryo-EM maps of proteins using constrained geometric simulations.
Recent experimental advances in producing density maps from cryo-electron microscopy (cryo-EM) have challenged theorists to develop improved techniques to provide structural models that are consistent with the data and that preserve all the local stereochemistry associated with the biomolecule. We develop a new technique that maintains the local geometry and chemistry at each stage of the fitti...
متن کاملPersistent topology for cryo-EM data analysis.
In this work, we introduce persistent homology for the analysis of cryo-electron microscopy (cryo-EM) density maps. We identify the topological fingerprint or topological signature of noise, which is widespread in cryo-EM data. For low signal-to-noise ratio (SNR) volumetric data, intrinsic topological features of biomolecular structures are indistinguishable from noise. To remove noise, we empl...
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ژورنال
عنوان ژورنال: Journal of Structural Biology
سال: 2019
ISSN: 1047-8477
DOI: 10.1016/j.jsb.2019.05.012